WastewaterSinglePathogen renamed WastewaterPathogenAgnostic

+ various grdi and Wastewater enum changes
cidgoh · Apr 5, 2024 · e0ca01d · e0ca01d
1 parent b582522
commit e0ca01d
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Showing 11 changed files with 8,417 additions and 5,899 deletions.
diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json
diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml
diff --git a/web/templates/grdi/schema_core.yaml b/web/templates/grdi/schema_core.yaml
@@ -1,7 +1,7 @@
 id: https://example.com/GRDI
 name: "GRDI"
 description: ""
-version: 9.0.0
+version: 10.0.0
 imports:
   - 'linkml:types'
 prefixes:

diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi/schema_enums.tsv
@@ -354,7 +354,7 @@ environmental_site menu		Abattoir [ENVO:01000925]
 		Artificial wetland [ENVO:03501406]										
 		Breeding ground [ENVO:03501441]										
 		Building [ENVO:00000073]										
-			Barn [EOL:0001898]									
+			Barn [ENVO:03501257]									
 				Breeder barn [ENVO:03501383]								
 				Broiler barn [ENVO:03501386]								
 				Sheep barn [ENVO:03501385]								
@@ -537,11 +537,11 @@ environmental_material menu		Air [ENVO:00002005]
 		Biosolids [ENVO:00002059]										
 		Boot [GSSO:012935]										
 			Boot cover [OBI:0002806]									
-		Broom [ENVO:03501377]										
+		Broom [ENVO:03501431]										
 		Bulk tank [ENVO:03501379]										
 		Chick box [AGRO:00000678]										
 		Chick pad [AGRO:00000672]										
-		Cleaning equipment [ENVO:03501376]										
+		Cleaning equipment [ENVO:03501430]										
 		Compost [ENVO:00002170]										
 		Contaminated water [ENVO:00002186]										
 			Fecal slurry [ENVO:03501436]									
@@ -574,8 +574,9 @@ environmental_material menu		Air [ENVO:00002005]
 			Agricultural soil [ENVO:00002259]									
 			Forest soil [ENVO:00002261]									
 		Straw [ENVO:00003869]										
-			Canola straw									
+			Canola straw [FOODON:00004430]									
 			Oat straw [FOODON:03309878]									
+			Barley straw [FOODON:00004559]									
 		Water [CHEBI:15377]										
 			Drinking water [ENVO:00003064]									
 			Groundwater [ENVO:01001004]									
@@ -632,7 +633,7 @@ anatomical_part menu		Carcass [UBERON:0008979]
 			Rectum [UBERON:0001052]									
 			Spleen [UBERON:0002106]									
 			Urinary bladder [UBERON:0001255]									
-		Foot [BTO:0000476]										
+		Foot [UBERON:0002387]										
 			Head [UBERON:0000033]									
 			Brain [UBERON:0000955]									
 			Ear [UBERON:0001690]									
@@ -776,9 +777,9 @@ food_product menu		Animal feed [ENVO:02000047]
 				Chicken meat (ground or minced, regular) [FOODON:03000404]								
 				Chicken meat (ground or minced, boneless) [FOODON:03000410]								
 			Chicken nugget [FOODON:00002672]									
-			Chicken thigh									
+			Chicken thigh  [FOODON:02020219]									
 				Chicken thigh (skinless) [FOODON:00003331]								
-				Chicken thigh (skinless, with bone)								
+				Chicken thigh (skinless, with bone) [FOODON:02020227]								
 				Chicken thigh (skinless, boneless) [FOODON:03000417]								
 					Chicken upper thigh [FOODON:03000381]							
 						Chicken upper thigh (with skin) [FOODON:03000383]						
@@ -815,7 +816,8 @@ food_product menu		Animal feed [ENVO:02000047]
 				Pepperoni [FOODON:03311003]								
 				Salami [FOODON:03312067]								
 			Shellfish [FOODON:03411433]									
-			Shrimp [FOODON:03411237]									
+				Shrimp [FOODON:03411237]								
+				Scallop [FOODON:03411489]								
 			Turkey breast [FOODON:00002690]									
 				Turkey breast (back off) [FOODON:03000386]								
 				Turkey breast (skinless) [FOODON:03000372]								
@@ -846,6 +848,8 @@ food_product menu		Animal feed [ENVO:02000047]
 		Nuts and seed products										
 			Almond (whole or parts) [FOODON:03000218]									
 				Almond (whole) [FOODON:00003523]								
+			Barley seed [FOODON:00003394]									
+			Canola seed [FOODON:00004560]									
 			Chia seed powder [FOODON:00003925]									
 			Chia seed (whole or parts) [FOODON:03000241]									
 			Flaxseed powder [FOODON:00004276]									
@@ -955,6 +959,9 @@ animal_source_of_food menu		Cow [NCBITaxon:9913]
 			Chicken [NCBITaxon:9031]									
 			Turkey [NCBITaxon:9103]									
 		Sheep [NCBITaxon:9940]										
+		Shellfish [FOODON:03411433]										
+			Scallop [NCBITaxon:6566]									
+			Shrimp [FOODON:03411237									
 
 
 food_product_production_stream menu		Beef cattle production stream [FOODON:03000452]										
@@ -1036,9 +1043,11 @@ host (common name) menu		Bird [NCBITaxon:8782]
 			Turkey [NCBITaxon:9103]									
 		Fish [FOODON:03411222]										
 			Rainbow Trout [NCBITaxon:8022]									
+			Sablefish [NCBITaxon:229290]									
 			Salmon [FOODON:00003473]									
 				Atlantic Salmon [NCBITaxon:8030]								
 				Chinook salmon [NCBITaxon:74940]								
+				Coho Salmon [NCBITaxon:8019]								
 		Mammal [FOODON:03411134]										
 			Companion animal [FOODON:03000300]									
 			Cow [NCBITaxon:9913]									
@@ -1051,7 +1060,8 @@ host (common name) menu		Bird [NCBITaxon:8782]
 			Blue Mussel [NCBITaxon:6550]									
 
 
-host (scientific name) menu		Bos taurus [NCBITaxon:9913]										
+host (scientific name) menu		Anoplopoma fimbria [NCBITaxon:229290]										
+		Bos taurus [NCBITaxon:9913]										
 		Crassostrea virginica [NCBITaxon:6565]										
 		Gallus gallus [NCBITaxon:9031]										
 		Grus americana [NCBITaxon:9117]										
@@ -1063,6 +1073,7 @@ host (scientific name) menu		Bos taurus [NCBITaxon:9913]
 		Larus marinus [NCBITaxon:8912]										
 		Meleagris gallopavo [NCBITaxon:9103]										
 		Mytilus edulis [NCBITaxon:6550]										
+		Oncorhynchus kisutch [NCBITaxon:8019]										
 		Oncorhynchus mykiss [NCBITaxon:8022]										
 		Oncorhynchus tshawytscha [NCBITaxon:74940]										
 		Ovis aries [NCBITaxon:9940]										
@@ -1216,6 +1227,7 @@ organism menu		Acinetobacter [NCBITaxon:469]
 		Pantoea [NCBITaxon:53335]										
 			Pantoea ananatis [NCBITaxon:553]									
 		Photobacterium [NCBITaxon:657]										
+			Photobacterium indicum[NCBITaxon:81447]									
 			Photobacterium sp. [NCBITaxon:660]									
 		Providencia [NCBITaxon:586]										
 			Providencia rettgeri [NCBITaxon:587]									
@@ -1228,6 +1240,7 @@ organism menu		Acinetobacter [NCBITaxon:469]
 			Pseudomonas sp. [NCBITaxon:306]									
 		Psychrobacter [NCBITaxon:497]										
 			Psychrobacter faecalis [NCBITaxon:180588]									
+			Psychrobacter nivimaris [NCBITaxon:281738]									
 			Psychrobacter sp. [NCBITaxon:56811]									
 		Rahnella [NCBITaxon:34037]										
 			Rahnella aquatilis [NCBITaxon:34038]									
@@ -1241,6 +1254,7 @@ organism menu		Acinetobacter [NCBITaxon:469]
 		Shewanella [NCBITaxon:22]										
 			Shewanella pealeana [NCBITaxon:70864]									
 			Shewanella putrefaciens [NCBITaxon:24]									
+			Shewanella oncorhynchi [NCBITaxon:2726434]									
 			Shewanella sp. [NCBITaxon:50422]									
 		Staphylococcus [NCBITaxon:1279]										
 			Staphylococcus aureus [NCBITaxon:1280]									
@@ -1270,6 +1284,7 @@ sequenced_by menu		Public Health Agency of Canada (PHAC) [GENEPIO:0100551]
 		Health Canada (HC) [GENEPIO:0100554]										
 		Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]										
 		Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]										
+		McGill University [GENEPIO:0101083]										
 
 
 purpose_of_sequencing menu		Cluster/Outbreak investigation [GENEPIO:0100001]										
@@ -1337,12 +1352,20 @@ sequencing_instrument menu		Illumina [GENEPIO:0100105]
 			DNBSEQ-G50 [GENEPIO:0100150]									
 
 
+sequencing_assay_type menu		Amplicon sequencing assay [OBI:0002767]										
+			16S ribosomal gene sequencing assay [OBI:0002763]									
+		Whole genome sequencing assay [OBI:0002117]										
+		Whole metagenome sequencing assay [OBI:0002623]										
+			Whole virome sequencing assay [OBI:0002768]									
+
+
 sequence_submitted_by menu		Public Health Agency of Canada (PHAC) [GENEPIO:0100551]										
 		Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]										
 		Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553]										
 		Health Canada (HC) [GENEPIO:0100554]										
 		Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]										
 		Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]										
+		McGill University [GENEPIO:0101083]										
 
 
 attribute_package menu		Pathogen.cl [GENEPIO:0001835]										

diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv
@@ -106,6 +106,7 @@ Multiple alternative isolate IDs can be provided, separated by semi-colons."	GHI
 	Sequence information	GENEPIO:0100472	sequencing_project_name		WhitespaceMinimizedString										The name of the project/initiative/program for which sequencing was performed.	Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value.	AMR-GRDI (PA-1356)	
 	Sequence information	GENEPIO:0100473	sequencing_platform		sequencing_platform menu	null value menu									The platform technology used to perform the sequencing.	Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.	Illumina [GENEPIO:0001923]	
 	Sequence information	GENEPIO:0001452	sequencing_instrument		sequencing_instrument menu	null value menu									The model of the sequencing instrument used.	Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.	Illumina HiSeq 2500 [GENEPIO:0100117]	
+	Sequence information	GENEPIO:0100997	sequencing_assay_type		sequencing_assay_type menu										The overarching sequencing methodology that was used to determine the sequence of a biomaterial.	Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value.	whole genome sequencing assay [OBI:0002117]	
 	Sequence information	GENEPIO:0001450	library_preparation_kit		WhitespaceMinimizedString										The name of the DNA library preparation kit used to generate the library being sequenced.	Provide the name of the library preparation kit used.	Nextera XT	
 	Sequence information	GENEPIO:0001454	sequencing_protocol		WhitespaceMinimizedString										The protocol or method used for sequencing.	Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online.	https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no	
 	Sequence information	GENEPIO:0001476	r1_fastq_filename		WhitespaceMinimizedString										The user-specified filename of the r1 FASTQ file.	Provide the r1 FASTQ filename.	ABC123_S1_L001_R1_001.fastq.gz	

diff --git a/web/templates/menu.json b/web/templates/menu.json
@@ -78,8 +78,8 @@
       "status": "published",
       "display": true
     },
-    "WastewaterSinglePathogen": {
-      "name": "WastewaterSinglePathogen",
+    "WastewaterPathogenAgnostic": {
+      "name": "WastewaterPathogenAgnostic",
       "status": "published",
       "display": true
     }