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feat(catalogue): extend Resources table to accomodate description of samples collected next to the data #4681

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feat(catalogue): extend Resources table to accomodate description of samples collected next to the data #4681

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f9c7052
Add attributes to Resources table
hslh Feb 5, 2025
311b6b5
Merge branch 'master' into feat-extend-resources-table
hslh Feb 6, 2025
bb7b192
Add table Resource qualities and accompanying ontologies
hslh Feb 6, 2025
3b90939
Add attributes to Resource counts
hslh Feb 6, 2025
fa788ee
Add relevant ontologies
hslh Feb 6, 2025
c0f2e00
Merge branch 'master' into feat-extend-resources-table
mswertz Feb 12, 2025
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13 changes: 13 additions & 0 deletions data/_models/shared/Resources.csv
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Expand Up @@ -15,6 +15,7 @@ Resources,,network type,ontology_array,,,CatalogueOntologies,Network types,,,,,T
Resources,,website,hyperlink,,,,,,,,"http://www.w3.org/ns/dcat#landingPage,foaf:homepage",Link to the website or homepage,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE"
Resources,,description,text,,,,,,,,http://purl.org/dc/terms/description,Short description,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE"
Resources,,keywords,string_array,,,,,,,,http://www.w3.org/ns/dcat#keyword,Keywords to increase findability of this resource. Try to use words that are not used in the description. Keywords are not displayed on the resource page,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,RWEStaging,UMCUCohorts,INTEGRATE"
Resources,,research domain,ontology_array,,,CatalogueOntologies,Research domains,,,,,The research domain(s) this resource is relevant to,"DataCatalogueFlat,CohortsStaging"
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Resources,,internal identifiers,refback,,,,Internal identifiers,,resource,,,Internal identifier(s) for this resource (e.g. UMCG register number),"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging"
Resources,,external identifiers,refback,,,,External identifiers,,resource,,,External identifier(s) for this resource (e.g. EUPASS number or BBMRI persistent identifer),"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,INTEGRATE"
Resources,,start year,int,,,,,,,,http://www.w3.org/ns/dcat#startDate,"The year when the resource started, e.g. when data or samples started to be collected or extracted, or when the resource was established","DataCatalogueFlat,EMA,RWEStaging,CohortsStaging,UMCGCohortsStaging,NetworksStaging,INTEGRATE"
Expand Down Expand Up @@ -48,6 +49,7 @@ Resources,,population of interest other,text,,,,,,,,,"If population of interest
Resources,,countries,ontology_array,,,CatalogueOntologies,Countries,,,,http://purl.org/dc/terms/spatial,Countries where data/samples from this resource largely originate from,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE"
Resources,,regions,ontology_array,,,CatalogueOntologies,Regions,,,,http://purl.org/dc/terms/spatial,Geographical regions where data/samples from this resource largely originate from,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE"
Resources,,population age groups,ontology_array,,,CatalogueOntologies,Age groups,,,,"urn:uuid:a7ef52b2-bd43-4294-a80f-3e7299af35e4#healthdcatap:minimumTypicalAge,urn:uuid:a7ef52b2-bd43-4294-a80f-3e7299af35e4#healthdcatap:maximumTypicalAge",Which population age groups are captured in this resource? Select all that are relevant,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE"
Resources,,sex types,ontology_array,,,CatalogueOntologies,Sex types,,,,http://purl.obolibrary.org/obo/PATO_0000047,The sex of the individuals in this resource - MIABIS-COLLECTION-08 (v3.0),"DataCatalogueFlat,CohortsStaging"
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Resources,,inclusion criteria,ontology_array,,,CatalogueOntologies,Inclusion Exclusion Criteria,,,,,Inclusion criteria applied to the participants of this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE"
Resources,,other inclusion criteria,text,,,,,,,,,Other inclusion criteria applied to the participants of this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE"
Resources,,exclusion criteria,ontology_array,,,CatalogueOntologies,Inclusion Exclusion Criteria,,,,,Exclusion criteria applied to the participants of this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE"
Expand All @@ -67,6 +69,9 @@ Resources,,people involved,refback,,,,Contacts,,resource,,http://www.w3.org/ns/d
Resources,,organisations involved,refback,,,,Organisations,,resource,,"http://purl.org/dc/terms/publisher,http://purl.org/dc/terms/creator",Organisations involved and their role(s),"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts,INTEGRATE"
Resources,,networks involved,refback,,,,Resources,,resources,,,The consortia or networks that this resource is part of,"DataCatalogueFlat,EMA"
Resources,,networks other,text,,,,,,,,,List the names of any other networks that are not listed and this resource is involved in,EMA
Resources,,"available data, imaging and samples,heading",,,,,,,,,,Data model and contents,"DataCatalogueFlat,EMA,RWEStaging,CohortsStaging,UMCGCohortsStaging"
Resources,,data categories,ontology_array,,,CatalogueOntologies,Data categories,,,,http://www.w3.org/ns/dcat#theme,Types of data collected in this resource,"DataCatalogueFlat,CohortsStaging"
Resources,,number of samples,int,,,,,,,,,Total number of samples included in this resource,"DataCatalogueFlat,CohortsStaging"
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Resources,,available data and samples,heading,,,,,,,,,Data model and contents,"DataCatalogueFlat,EMA,RWEStaging,CohortsStaging"
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zit deze heading er nu 2x in? Is dat handig? op regel 72 en 75 is nu min of meer hetzelfde. Voorstel samenvoegen en hernoemen? Of zie je dat anders?

Resources,,datasets,refback,,,,Datasets,,resource,,,List of datasets contained in this resouce if applicable,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging"
Resources,,samplesets,refback,,,,Samplesets,,resource,,,List of sample sets contained in this resource if applicable,"DataCatalogueFlat,CohortsStaging,RWEStaging,StudiesStaging"
Expand All @@ -86,6 +91,11 @@ Resources,,diagnosis medical event vocabulary other,text,,,,,,,,,"If 'other', wh
Resources,,data dictionary available,bool,,,,,,,,,Are a data dictionary and a data model available?,"DataCatalogueFlat,RWEStaging"
Resources,,disease details,ontology_array,,,CatalogueOntologies,MedDRA,,,,,"If data on a specific disease is collected, which diseases does the data source collect information on","DataCatalogueFlat,EMA,RWEStaging"
Resources,,disease details other,text,,,,,,,,,Specify disease details if not present in MedDRA,EMA
Resources,,biospecimen types,ontology_array,,,CatalogueOntologies,BiospecimenType,,,,,"If the data bank contains biospecimens, what types of specimen","DataCatalogueFlat,CohortsStaging"
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is biospecimen types niet hetzelfde als material types? Of hebben we die alleen op collection event? In any case graag gelijk houden.

Resources,,sample storage temperatures,ontology_array,,,CatalogueOntologies,Storage temperatures,,,,,"The long-term storage temperature at which the sample is stored after preparation, based on SPREC v3 - MIABIS-COLLECTION-15 (v3.0)","DataCatalogueFlat,CohortsStaging"
Resources,,image types,ontology_array,,,CatalogueOntologies,Image types,,,,,Types of imaging data collected in this resource,"DataCatalogueFlat,CohortsStaging"
Resources,,imaging modality,ontology_array,,,CatalogueOntologies,Imaging modalities,,,,,Imaging modalities used in this resource,"DataCatalogueFlat,CohortsStaging"
Resources,,imaging body parts,ontology_array,,,CatalogueOntologies,Body parts,,,,,The body parts examined during imaging,"DataCatalogueFlat,CohortsStaging"
Resources,,biospecimen collected,ontology_array,,,CatalogueOntologies,Biospecimens,,,,,"If the data bank contains biospecimens, what types of specimen","DataCatalogueFlat,RWEStaging"
Resources,,languages,ontology_array,,,CatalogueOntologies,Languages,,,,,Languages that the records are recorded in (ISO 639),"DataCatalogueFlat,EMA,RWEStaging"
Resources,,multiple entries,bool,,,,,,,,,Can there be multiple entries for a single person in the data bank?,"DataCatalogueFlat,RWEStaging"
Expand Down Expand Up @@ -116,6 +126,8 @@ Resources,,access non EU,bool,,,,,,,,,Can (an extract of) the data bank be acces
Resources,,access non EU conditions,text,,,,,,,,,"If yes to the above, describe the conditions under which non-EU/EEA access may be granted","DataCatalogueFlat,RWEStaging"
Resources,,biospecimen access,bool,,,,,,,,,"If the data bank contains biospecimens (e.g. tissue samples), can these be retrieved?","DataCatalogueFlat,EMA,RWEStaging,INTEGRATE"
Resources,,biospecimen access conditions,text,,,,,,,,,"If yes to the above, describe the conditions under which permission to retrieve biospecimens may be granted","DataCatalogueFlat,EMA,RWEStaging,INTEGRATE"
Resources,,biospecimen access,bool,,,,,,,,,"If the data bank contains imaging data, can these be accessed?","DataCatalogueFlat,CohortsStaging"
Resources,,biospecimen access conditions,text,,,,,,,,,"If yes to the above, describe the conditions under which access to imaging data can be granted","DataCatalogueFlat,CohortsStaging"
Resources,,governance details,text,,,,,,,,,"If available, provide a link to documents or webpages that describe the overall governance of the data source bank (governing data access or utilisation for research purposes by existing DAPs)","DataCatalogueFlat,RWEStaging"
Resources,,approval for publication,bool,,,,,,,,,Is an approval needed to publish the results of a study using the data,"DataCatalogueFlat,EMA,RWEStaging"
Resources,,updates,heading,,,,,,,,,Information on the regularity of updates and time lags,"DataCatalogueFlat,EMA,RWEStaging"
Expand All @@ -133,6 +145,7 @@ Resources,,quality,heading,,,,,,,,,List of relevant studies conducted using the
Resources,,standard operating procedures,bool,,,,,,,,,Is there a standard operating procedure document that defines the processes and procedures for data capture and management?,"DataCatalogueFlat,RWEStaging"
Resources,,qualification,bool,,,,,,,,,"Has the data source successfully undergone a formal qualification process (e.g. from the EMA, ISO or other certifications)?","DataCatalogueFlat,EMA,RWEStaging,INTEGRATE"
Resources,,qualifications description,text,,,,,,,,,"Has the data source successfully undergone a qualification process (e.g. from the EMA)? If yes, describe the qualification(s) granted","DataCatalogueFlat,EMA,RWEStaging"
Resources,,qualifications,refback,,,,Resource qualities,,resource,,,Quality standards that this resource meets,"DataCatalogueFlat,CohortsStaging"
Resources,,audit possible,bool,,,,,,,,,"Are external parties allowed to audit the data? For example, is it possible for an external party to audit the quality or validity of the data source?","DataCatalogueFlat,RWEStaging"
Resources,,completeness,text,,,,,,,,,Describe the completeness of the data bank (e.g. variables with more or fewer missing values),"DataCatalogueFlat,RWEStaging"
Resources,,completeness over time,text,,,,,,,,,Describe any changes in completeness of the data bank (e.g. variables with more or fewer missing values) that have occurred over time,"DataCatalogueFlat,RWEStaging"
Expand Down
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