diff --git a/apps/central/src/components/SchemaCreateModal.vue b/apps/central/src/components/SchemaCreateModal.vue index 87e18bd6e5..8482e6772a 100644 --- a/apps/central/src/components/SchemaCreateModal.vue +++ b/apps/central/src/components/SchemaCreateModal.vue @@ -143,6 +143,7 @@ export default { "DATA_CATALOGUE_NETWORK_STAGING", "UMCG_COHORT_STAGING", "UMCU_COHORTS_STAGING", + "INTEGRATE_COHORTS_STAGING", "RD3", "JRC_COMMON_DATA_ELEMENTS", "FAIR_GENOMES", diff --git a/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/DataModels.java b/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/DataModels.java index e2a7cfabc0..c45a3cd6f3 100644 --- a/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/DataModels.java +++ b/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/DataModels.java @@ -15,6 +15,7 @@ public enum Profile { DATA_CATALOGUE_AGGREGATES("_profiles/DataCatalogueAggregates.yaml"), UMCG_COHORT_STAGING("_profiles/UMCGCohortsStaging.yaml"), UMCU_COHORTS_STAGING("_profiles/UMCUCohorts.yaml"), + INTEGRATE_COHORTS_STAGING("_profiles/INTEGRATECohorts.yaml"), FAIR_DATA_HUB("_profiles/FAIRDataHub.yaml"), RD3("_profiles/RD3.yaml"), JRC_COMMON_DATA_ELEMENTS("_profiles/JRC-CDE.yaml"), diff --git a/data/_models/shared/Collection events.csv b/data/_models/shared/Collection events.csv index 6f0d9bcf2a..44674bfc9d 100644 --- a/data/_models/shared/Collection events.csv +++ b/data/_models/shared/Collection events.csv @@ -1,16 +1,16 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles,visible -Collection events,,,,,,,,,,,dct:PeriodOfTime,Definition of a collection event for a resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,NetworksStaging,UMCUCohorts", -Collection events,,resource,ref,1,TRUE,,Resources,,,,"dct:isPartOf,dct:inSeries",Resource this collection event is part of,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,NetworksStaging,UMCUCohorts", -Collection events,,name,,1,TRUE,,,,,,"dct:title,dct:identifier",Name of the collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,NetworksStaging,UMCUCohorts", -Collection events,,description,text,,,,,,,,dct:description,Description of the collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,NetworksStaging,UMCUCohorts", -Collection events,,subpopulations,ref_array,,,,Subpopulations,resource,,,dct:references,Subpopulations that are targetted by this collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", -Collection events,,start date,date,,,,,,,,dcat:startDate,Start date of data collection,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts", -Collection events,,end date,date,,,,,,,,dcat:endDate,End date of data collection. Leave empty if collection is ongoing,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts", -Collection events,,age groups,ontology_array,,,CatalogueOntologies,Age groups,,,,,Age groups included in this data collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,NetworksStaging,UMCUCohorts", -Collection events,,number of participants,int,,,,,,,,,Number of participants sampled in this data collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts", -Collection events,,areas of information,ontology_array,,,CatalogueOntologies,Areas of information cohorts,,,,,Areas of information that were extracted in this data collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts", -Collection events,,data categories,ontology_array,,,CatalogueOntologies,Data categories,,,,dcat:theme,Methods of data collection used in this collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts", -Collection events,,sample categories,ontology_array,,,CatalogueOntologies,Sample categories,,,,dcat:theme,Samples that were collected in this collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts", -Collection events,,standardized tools,ontology_array,,,CatalogueOntologies,Standardized tools,,,,,"Standardized tools, e.g. surveys, questionnaires, instruments used to collect data for this collection event","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts", -Collection events,,standardized tools other,,,,,,,,,,"If 'other', please specify","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts", -Collection events,,core variables,string_array,,,,,,,,,Name 10-20 relevant variables that were collected in this collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts", +Collection events,,,,,,,,,,,dct:PeriodOfTime,Definition of a collection event for a resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,NetworksStaging,UMCUCohorts,INTEGRATE", +Collection events,,resource,ref,1,TRUE,,Resources,,,,"dct:isPartOf,dct:inSeries",Resource this collection event is part of,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,NetworksStaging,UMCUCohorts,INTEGRATE", +Collection events,,name,,1,TRUE,,,,,,"dct:title,dct:identifier",Name of the collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,NetworksStaging,UMCUCohorts,INTEGRATE", +Collection events,,description,text,,,,,,,,dct:description,Description of the collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,NetworksStaging,UMCUCohorts,INTEGRATE", +Collection events,,subpopulations,ref_array,,,,Subpopulations,resource,,,dct:references,Subpopulations that are targetted by this collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Collection events,,start date,date,,,,,,,,dcat:startDate,Start date of data collection,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts,INTEGRATE", +Collection events,,end date,date,,,,,,,,dcat:endDate,End date of data collection. Leave empty if collection is ongoing,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts,INTEGRATE", +Collection events,,age groups,ontology_array,,,CatalogueOntologies,Age groups,,,,,Age groups included in this data collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,NetworksStaging,UMCUCohorts,INTEGRATE", +Collection events,,number of participants,int,,,,,,,,,Number of participants sampled in this data collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts,INTEGRATE", +Collection events,,areas of information,ontology_array,,,CatalogueOntologies,Areas of information cohorts,,,,,Areas of information that were extracted in this data collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts,INTEGRATE", +Collection events,,data categories,ontology_array,,,CatalogueOntologies,Data categories,,,,dcat:theme,Methods of data collection used in this collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts,INTEGRATE", +Collection events,,sample categories,ontology_array,,,CatalogueOntologies,Sample categories,,,,dcat:theme,Samples that were collected in this collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts,INTEGRATE", +Collection events,,standardized tools,ontology_array,,,CatalogueOntologies,Standardized tools,,,,,"Standardized tools, e.g. surveys, questionnaires, instruments used to collect data for this collection event","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts,INTEGRATE", +Collection events,,standardized tools other,,,,,,,,,,"If 'other', please specify","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts,INTEGRATE", +Collection events,,core variables,string_array,,,,,,,,,Name 10-20 relevant variables that were collected in this collection event,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,StudiesStaging,UMCUCohorts,INTEGRATE", diff --git a/data/_models/shared/Contacts.csv b/data/_models/shared/Contacts.csv index 418d8fd42f..f9cfdec80a 100644 --- a/data/_models/shared/Contacts.csv +++ b/data/_models/shared/Contacts.csv @@ -1,19 +1,19 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles,visible,computed -Contacts,,,,,,,,,,,vcard:Kind,Listing of contact persons per resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts",, -Contacts,,resource,ref,1,TRUE,,Resources,,,,,Resource the contact is affiliated with,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts",, -Contacts,,role,ontology_array,,,CatalogueOntologies,Contribution types,,,,vcard:hasRole,Type(s) of contribution or role in the resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts",, -Contacts,,role description,text,,,,,,,,,Description of the role,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCUCohorts",, -Contacts,,first name,,1,TRUE,,,,,,foaf:firstName,First name of the contact person,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts",, -Contacts,,last name,,1,TRUE,,,,,,foaf:familyName,Last name of the contact person,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts",, +Contacts,,,,,,,,,,,vcard:Kind,Listing of contact persons per resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE",, +Contacts,,resource,ref,1,TRUE,,Resources,,,,,Resource the contact is affiliated with,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE",, +Contacts,,role,ontology_array,,,CatalogueOntologies,Contribution types,,,,vcard:hasRole,Type(s) of contribution or role in the resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE",, +Contacts,,role description,text,,,,,,,,,Description of the role,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCUCohorts,INTEGRATE",, +Contacts,,first name,,1,TRUE,,,,,,foaf:firstName,First name of the contact person,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE",, +Contacts,,last name,,1,TRUE,,,,,,foaf:familyName,Last name of the contact person,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE",, Contacts,,display name,,,TRUE,,,,,,"foaf:name,vcard:hasName",Display name of the contact person,DataCatalogueFlat,FALSE,firstName+' '+lastName Contacts,,statement of consent personal data,bool,,TRUE,,,,,,,"Indicate whether this person consents to display the following personal data in the catalogue (which is openly accessible): title, name, photo, orcid ID, institute, department, expertise, discipline and role within the resource. These data-items may partly be extracted from the UMCG and/or RUG employee pages. The consent also includes future linkages with other national and international catalogues and platforms to increase visibility and findability (e.g. BBMRI-ERIC, NARCIS) of UMCG-resources. Contributors without a positive statement of consent will not be shown in the UMCG Research Data Catalogue",UMCGCohortsStaging,, -Contacts,,prefix,,,,,,,,,,"Surname prefix, if applicable","DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts",, -Contacts,,initials,,,,,,,,,,Initials of the contact person,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts",, -Contacts,,title,ontology,,,CatalogueOntologies,Titles,,,,foaf:title,Title of the contact person,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts",, -Contacts,,organisation,ref,,,,Organisations,resource,,,foaf:Organization,Affiliated organisation of the contact person,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts",, -Contacts,,email,,,,,,,,,"vcard:hasEmail,foaf:mbox",Contact's email address,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts",, +Contacts,,prefix,,,,,,,,,,"Surname prefix, if applicable","DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE",, +Contacts,,initials,,,,,,,,,,Initials of the contact person,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE",, +Contacts,,title,ontology,,,CatalogueOntologies,Titles,,,,foaf:title,Title of the contact person,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE",, +Contacts,,organisation,ref,,,,Organisations,resource,,,foaf:Organization,Affiliated organisation of the contact person,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE",, +Contacts,,email,,,,,,,,,"vcard:hasEmail,foaf:mbox",Contact's email address,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE",, Contacts,,statement of consent email,bool,,TRUE,,,,,,,"Indicate whether this person consents to display their email address in the catalogue (which is openly accessible). The consent also includes future linkages with other national and international catalogues and platforms to increase visibility and findability (e.g. BBMRI-ERIC, NARCIS) of UMCG-resources. Contributors without a positive statement of consent for their email address will be shown without their email address in the UMCG Research Data Catalogue",UMCGCohortsStaging,, -Contacts,,orcid,,,,,,,,,,Orcid of the contact person,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts",, +Contacts,,orcid,,,,,,,,,,Orcid of the contact person,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE",, Contacts,,homepage,,,,,,,,,foaf:workplaceHomepage,Link to contact's homepage,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging",, Contacts,,photo,file,,,,,,,,foaf:img,Contact's photograph,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging",, -Contacts,,expertise,,,,,,,,,,Description of contact's expertise,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging",, +Contacts,,expertise,,,,,,,,,,Description of contact's expertise,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,INTEGRATE",, diff --git a/data/_models/shared/Documentation.csv b/data/_models/shared/Documentation.csv index 6db7f071ca..6388899667 100644 --- a/data/_models/shared/Documentation.csv +++ b/data/_models/shared/Documentation.csv @@ -1,8 +1,8 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles,visible -Documentation,,,,,,,,,,,,Documentation attached to a resource,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Documentation,,resource,ref,1,TRUE,,Resources,,,,,The resource this documentation is for,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Documentation,,name,,1,TRUE,,,,,,,Document name,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Documentation,,type,ontology,,,CatalogueOntologies,Document types,,,,,Type of documentation,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Documentation,,description,text,,,,,,,,,Description of the document,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Documentation,,url,hyperlink,,,,,,,,,Hyperlink to the source of the documentation,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Documentation,,file,file,,,,,,,,,Optional file attachment containing the documentation,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", +Documentation,,,,,,,,,,,,Documentation attached to a resource,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Documentation,,resource,ref,1,TRUE,,Resources,,,,,The resource this documentation is for,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Documentation,,name,,1,TRUE,,,,,,,Document name,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Documentation,,type,ontology,,,CatalogueOntologies,Document types,,,,,Type of documentation,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Documentation,,description,text,,,,,,,,,Description of the document,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Documentation,,url,hyperlink,,,,,,,,,Hyperlink to the source of the documentation,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Documentation,,file,file,,,,,,,,,Optional file attachment containing the documentation,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", diff --git a/data/_models/shared/External identifiers.csv b/data/_models/shared/External identifiers.csv index 178123d86a..d3c663638c 100644 --- a/data/_models/shared/External identifiers.csv +++ b/data/_models/shared/External identifiers.csv @@ -1,6 +1,6 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles,visible -External identifiers,,,,,,,,,,,,External identifier(s) for this resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -External identifiers,,resource,ref,1,TRUE,,Resources,,,,,Resource that this external identifier belongs to,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -External identifiers,,identifier,text,1,TRUE,,,,,,,External identifier,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -External identifiers,,external identifier type,ontology,,,CatalogueOntologies,External identifier types,,,,,External identifier type,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -External identifiers,,external identifier type other,text,,,,,,,,,"If 'other', enter external identifier type","DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", +External identifiers,,,,,,,,,,,,External identifier(s) for this resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +External identifiers,,resource,ref,1,TRUE,,Resources,,,,,Resource that this external identifier belongs to,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +External identifiers,,identifier,text,1,TRUE,,,,,,,External identifier,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +External identifiers,,external identifier type,ontology,,,CatalogueOntologies,External identifier types,,,,,External identifier type,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +External identifiers,,external identifier type other,text,,,,,,,,,"If 'other', enter external identifier type","DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", diff --git a/data/_models/shared/Organisations.csv b/data/_models/shared/Organisations.csv index eb6600fc7e..1734d30bf6 100644 --- a/data/_models/shared/Organisations.csv +++ b/data/_models/shared/Organisations.csv @@ -1,12 +1,12 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles,visible -Organisations,,,,,,,,,,,"org:Organization,foaf:Agent",Research departments and research groups. Null values will be generated from RoR,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Organisations,,resource,ref,1,TRUE,,Resources,,,,dcterms:isPartOf,Resource that this organisation is part of,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Organisations,,id,,1,TRUE,,,,,,dcterms:identifier,Internal identifier,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Organisations,,pid,hyperlink,,,,,,,,dcterms:identifier,"Persistent identifier, ideally from ROR","DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Organisations,,name,text,,TRUE,,,,,,"dcterms:title,foaf:name",Name used in (inter)national projects,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Organisations,,acronym,,,,,,,,,dcterms:identifier,"Acronym, if applicable","DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Organisations,,logo,file,,,,,,,,,Logo of the organisation,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging", -Organisations,,country,ontology_array,,,CatalogueOntologies,Countries,,,,vcard:country-name,Country in which the institution head office or coordinating centre is located,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Organisations,,website,hyperlink,,,,,,,,dcat:landingPage,Link to the website or homepage,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Organisations,,role,ontology_array,,,CatalogueOntologies,Organisation roles,,,,vcard:hasRole,Type(s) of contribution or role in the resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Organisations,,is lead organisation,bool,,,,,,,,,Whether the organisation is the lead organisation of this resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", +Organisations,,,,,,,,,,,"org:Organization,foaf:Agent",Research departments and research groups. Null values will be generated from RoR,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Organisations,,resource,ref,1,TRUE,,Resources,,,,dcterms:isPartOf,Resource that this organisation is part of,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Organisations,,id,,1,TRUE,,,,,,dcterms:identifier,Internal identifier,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Organisations,,pid,hyperlink,,,,,,,,dcterms:identifier,"Persistent identifier, ideally from ROR","DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Organisations,,name,text,,TRUE,,,,,,"dcterms:title,foaf:name",Name used in (inter)national projects,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Organisations,,acronym,,,,,,,,,dcterms:identifier,"Acronym, if applicable","DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Organisations,,logo,file,,,,,,,,,Logo of the organisation,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,INTEGRATE", +Organisations,,country,ontology_array,,,CatalogueOntologies,Countries,,,,vcard:country-name,Country in which the institution head office or coordinating centre is located,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Organisations,,website,hyperlink,,,,,,,,dcat:landingPage,Link to the website or homepage,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Organisations,,role,ontology_array,,,CatalogueOntologies,Organisation roles,,,,vcard:hasRole,Type(s) of contribution or role in the resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Organisations,,is lead organisation,bool,,,,,,,,,Whether the organisation is the lead organisation of this resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", diff --git a/data/_models/shared/Publications.csv b/data/_models/shared/Publications.csv index 9eb1de36c7..7e41afda0d 100644 --- a/data/_models/shared/Publications.csv +++ b/data/_models/shared/Publications.csv @@ -1,7 +1,7 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles,visible -Publications,,,,,,,,,,,,Publications based on doi,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Publications,,resource,ref,1,TRUE,,Resources,,,,dcterms:isPartOf,Resource that this publication is part of,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Publications,,doi,hyperlink,1,TRUE,,,,,,,Digital object identifier,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Publications,,title,,,TRUE,,,,,,,Publication title,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Publications,,is design publication,bool,,,,,,,,,Whether this publication is a marker or design publication,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts", -Publications,,reference,text,,,,,,,,,Formatted reference string (we aim to have this autogenerated),"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCUCohorts", +Publications,,,,,,,,,,,,Publications based on doi,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Publications,,resource,ref,1,TRUE,,Resources,,,,dcterms:isPartOf,Resource that this publication is part of,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Publications,,doi,hyperlink,1,TRUE,,,,,,,Digital object identifier,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Publications,,title,,,TRUE,,,,,,,Publication title,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Publications,,is design publication,bool,,,,,,,,,Whether this publication is a marker or design publication,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Publications,,reference,text,,,,,,,,,Formatted reference string (we aim to have this autogenerated),"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCUCohorts,INTEGRATE", diff --git a/data/_models/shared/Resource counts.csv b/data/_models/shared/Resource counts.csv index d0263f8832..cd58def91e 100644 --- a/data/_models/shared/Resource counts.csv +++ b/data/_models/shared/Resource counts.csv @@ -1,11 +1,11 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles,visible -Resource counts,,,,,,,,,,,,Quantitative information on the resource,"DataCatalogueFlat,RWEStaging,StudiesStaging", -Resource counts,,resource,ref,1,,,Resources,,,,,Resource id,"DataCatalogueFlat,RWEStaging,StudiesStaging", -Resource counts,,age group,ontology,1,,CatalogueOntologies,Age groups,,,,,Select the relevant age group for this quantitative information,"DataCatalogueFlat,RWEStaging,StudiesStaging", -Resource counts,,population size,int,,,,,,,,,"Total number of unique individuals with records captured in the data source (most recent count). In the catalogue, this will accommodate counts per year","DataCatalogueFlat,RWEStaging,StudiesStaging", +Resource counts,,,,,,,,,,,,Quantitative information on the resource,"DataCatalogueFlat,RWEStaging,StudiesStaging,INTEGRATE", +Resource counts,,resource,ref,1,,,Resources,,,,,Resource id,"DataCatalogueFlat,RWEStaging,StudiesStaging,INTEGRATE", +Resource counts,,age group,ontology,1,,CatalogueOntologies,Age groups,,,,,Select the relevant age group for this quantitative information,"DataCatalogueFlat,RWEStaging,StudiesStaging,INTEGRATE", +Resource counts,,population size,int,,,,,,,,,"Total number of unique individuals with records captured in the data source (most recent count). In the catalogue, this will accommodate counts per year","DataCatalogueFlat,RWEStaging,StudiesStaging,INTEGRATE", Resource counts,,active size,int,,,,,,,,,"Number of unique, active, or currently registered individuals with records captured in the data source (most recent count). In the catalogue, this will accommodate counts per year","DataCatalogueFlat,RWEStaging,StudiesStaging", Resource counts,,no individuals with samples,int,,,,,,,,,"Number of unique individuals with records of biological samples (e.g., blood, urine) (most recent count). In the catalogue, this will accommodate counts per year ","DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging", Resource counts,,mean observation years,int,,,,,,,,,Median years for which unique individuals with records captured in the data source are observable (most recent count),"DataCatalogueFlat,RWEStaging,StudiesStaging", Resource counts,,mean years active,int,,,,,,,,,Median time for which unique individuals with records captured in the data source are observable (most recent count),"DataCatalogueFlat,RWEStaging,StudiesStaging", -Resource counts,,median age,int,,,,,,,,,Median age of individuals within data source,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging", -Resource counts,,proportion female,int,,,,,,,,,Proportion of females in the data source,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging", +Resource counts,,median age,int,,,,,,,,,Median age of individuals within data source,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,INTEGRATE", +Resource counts,,proportion female,int,,,,,,,,,Proportion of females in the data source,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,INTEGRATE", diff --git a/data/_models/shared/Resources.csv b/data/_models/shared/Resources.csv index 0f63c54b78..4950e9b1be 100644 --- a/data/_models/shared/Resources.csv +++ b/data/_models/shared/Resources.csv @@ -1,70 +1,70 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles -Resources,,,,,,,,,,,"dcat:DatasetSeries,dcat:Dataset",Resource of data and/or samples. Use 'resource type' to specify,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,overview,heading,,,,,,,,,General information,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,id,,1,TRUE,,,,,,dct:identifier,Internal identifier,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,pid,,2,,,,,,,dct:identifier,Persistent identifier,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,name,text,3,TRUE,,,,,,dct:title,Name used in international projects,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" +Resources,,,,,,,,,,,"dcat:DatasetSeries,dcat:Dataset",Resource of data and/or samples. Use 'resource type' to specify,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,overview,heading,,,,,,,,,General information,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,id,,1,TRUE,,,,,,dct:identifier,Internal identifier,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,pid,,2,,,,,,,dct:identifier,Persistent identifier,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,name,text,3,TRUE,,,,,,dct:title,Name used in international projects,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,local name,,,,,,,,,rdfs:label,"If different from above, name in the national language","DataCatalogueFlat,CohortsStaging,RWEStaging" -Resources,,acronym,,,,,,,,,dct:alternative,"Acronym, if applicable","DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,type,ontology_array,,TRUE,CatalogueOntologies,Resource types,,,,,"Type of resource, e.g. registry, cohort, biobank","DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" +Resources,,acronym,,,,,,,,,dct:alternative,"Acronym, if applicable","DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,type,ontology_array,,TRUE,CatalogueOntologies,Resource types,,,,,"Type of resource, e.g. registry, cohort, biobank","DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,type other,,,,,,,,,,"If other, describe the type of resource","DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,StudiesStaging,UMCUCohorts" -Resources,,cohort type,ontology_array,,,CatalogueOntologies,Cohort study types,,,,,Type of cohort,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" +Resources,,cohort type,ontology_array,,,CatalogueOntologies,Cohort study types,,,,,Type of cohort,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,clinical study type,ontology_array,,,CatalogueOntologies,Clinical study types,,,,,Type of clinical study,"DataCatalogueFlat,EMA" Resources,,RWD type,ontology_array,,,CatalogueOntologies,Datasource types,,,,,Type of registry or health record,"DataCatalogueFlat,EMA,RWEStaging" Resources,,network type,ontology_array,,,CatalogueOntologies,Network types,,,,,Type of network,"DataCatalogueFlat,NetworksStaging" -Resources,,website,hyperlink,,,,,,,,dcat:landingPage,Link to the website or homepage,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,description,text,,,,,,,,dct:description,Short description,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,keywords,string_array,,,,,,,,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" +Resources,,website,hyperlink,,,,,,,,dcat:landingPage,Link to the website or homepage,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,description,text,,,,,,,,dct:description,Short description,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,keywords,string_array,,,,,,,,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,,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" -Resources,,start year,int,,,,,,,,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" -Resources,,end year,int,,,,,,,,dcat:endDate,"The year the resource ceased, e.g. when data or sample collection was stopped","DataCatalogueFlat,EMA,RWEStaging,CohortsStaging,UMCGCohortsStaging,NetworksStaging" +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,,,,,,,,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" +Resources,,end year,int,,,,,,,,dcat:endDate,"The year the resource ceased, e.g. when data or sample collection was stopped","DataCatalogueFlat,EMA,RWEStaging,CohortsStaging,UMCGCohortsStaging,NetworksStaging,INTEGRATE" Resources,,time span description,text,,,,,,,,,Description of time span,"DataCatalogueFlat,RWEStaging" -Resources,,contact email,,,,,,,,,dcat:contactPoint,Contact e-mail address ,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging" -Resources,,logo,file,,,,,,,,,"Logo of the resource, for use on homepages etc.","DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" +Resources,,contact email,,,,,,,,,dcat:contactPoint,Contact e-mail address ,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,INTEGRATE" +Resources,,logo,file,,,,,,,,,"Logo of the resource, for use on homepages etc.","DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,status,ontology,,,CatalogueOntologies,Study status,,,,,Status of the study,"DataCatalogueFlat,EMA,StudiesStaging" -Resources,,license,hyperlink,,,,,,,,dct:license,A legal document under which this catalogue record is made available,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,design and structure,heading,,,,,,,,,Structure of the resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,design,ontology,,,CatalogueOntologies,Cohort designs,,,,,"The study design of this cohort, i.e. cross-sectional or longitudinal","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,design description,text,,,,,,,,,"Short description of the study design of this resource, if applicable","DataCatalogueFlat,EMA,RWEStaging,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" +Resources,,license,hyperlink,,,,,,,,dct:license,A legal document under which this catalogue record is made available,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,design and structure,heading,,,,,,,,,Structure of the resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,design,ontology,,,CatalogueOntologies,Cohort designs,,,,,"The study design of this cohort, i.e. cross-sectional or longitudinal","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,design description,text,,,,,,,,,"Short description of the study design of this resource, if applicable","DataCatalogueFlat,EMA,RWEStaging,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,design schematic,file,,,,,,,,,A schematic depiction of the study design of this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,data collection type,ontology_array,,,CatalogueOntologies,Cohort collection types,,,,,Retrospective or prospective data collection,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" +Resources,,data collection type,ontology_array,,,CatalogueOntologies,Cohort collection types,,,,,Retrospective or prospective data collection,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,data collection description,text,,,,,,,,,Describe the process of collection and recording of data,"DataCatalogueFlat,EMA,RWEStaging" Resources,,reason sustained,text,,,,,,,,,"Description of the reason why the data bank is sustained by the organisation (e.g. for surveillance, clinical purposes, financial or administrative purposes, research purposes)","DataCatalogueFlat,RWEStaging" -Resources,,record trigger,text,,,,,,,,,"What triggers the creation of a record in the data bank? e.g. planned collection events, hospital discharge, specialist encounter, dispensation of a medicinal product, recording of a congenital anomaly","DataCatalogueFlat,EMA,RWEStaging" +Resources,,record trigger,text,,,,,,,,,"What triggers the creation of a record in the data bank? e.g. planned collection events, hospital discharge, specialist encounter, dispensation of a medicinal product, recording of a congenital anomaly","DataCatalogueFlat,EMA,RWEStaging,INTEGRATE" Resources,,unit of observation,text,,,,,,,,,"Based on the record trigger or promt, what is the unit(s) of observation of a record (e.g. person, prescription)?","DataCatalogueFlat,RWEStaging" -Resources,,subpopulations,refback,,,,Subpopulations,,resource,,,"List of cohorts or subpopulations defined in this resource, if applicable","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts" -Resources,,collection events,refback,,,,Collection events,,resource,,dcterms:hasPart,"List of data/sample collection events defined for this collection, if applicable","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts" +Resources,,subpopulations,refback,,,,Subpopulations,,resource,,,"List of cohorts or subpopulations defined in this resource, if applicable","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts,INTEGRATE" +Resources,,collection events,refback,,,,Collection events,,resource,,dcterms:hasPart,"List of data/sample collection events defined for this collection, if applicable","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts,INTEGRATE" Resources,,resources,ref_array,,,,Resources,,,,dct:dataset,List of other resources included in this resource,"DataCatalogueFlat,EMA" Resources,,part of resources,refback,,,,Resources,,resources,,dct:dataset,List of other collections included in this resource,"DataCatalogueFlat,EMA" Resources,,resources,ref_array,,,catalogue,Resources,,,,,"List of other resources included in this network, e.g. cohorts, biobanks or other networks",NetworksStaging -Resources,,population,heading,,,,,,,,,Description of the population that is sampled in this resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,number of participants,int,,,,,,,,,Total number of individuals for which data is collected,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,number of participants with samples,int,,,,,,,,,Number of individuals for which samples are collected,"DataCatalogueFlat,CohortsStaging,RWEStaging,UMCGCohortsStaging" +Resources,,population,heading,,,,,,,,,Description of the population that is sampled in this resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,number of participants,int,,,,,,,,,Total number of individuals for which data is collected,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,number of participants with samples,int,,,,,,,,,Number of individuals for which samples are collected,"DataCatalogueFlat,CohortsStaging,RWEStaging,UMCGCohortsStaging,INTEGRATE" Resources,,underlying population,text,,,,,,,,,Provide a summary description of the underlying population from which participants are sampled,"DataCatalogueFlat,RWEStaging" Resources,,population description,text,,,,,,,,,A short description of the study population,EMA Resources,,population of interest,ontology_array,,,CatalogueOntologies,Population of interest,,,,,Select population of interest,"DataCatalogueFlat,EMA,StudiesStaging" Resources,,population of interest other,text,,,,,,,,,"If population of interest is 'Other', please specify which other population has been studied","DataCatalogueFlat,EMA,StudiesStaging" -Resources,,countries,ontology_array,,,CatalogueOntologies,Countries,,,,dct:spatial,Countries where data/samples from this resource largely originate from,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,regions,ontology_array,,,CatalogueOntologies,Regions,,,,dct:spatial,Geographical regions where data/samples from this resource largely originate from,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,population age groups,ontology_array,,,CatalogueOntologies,Age groups,,,,,Which population age groups are captured in this resource? Select all that are relevant,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,inclusion criteria,ontology_array,,,CatalogueOntologies,Inclusion Exclusion Criteria,,,,,Inclusion criteria applied to the participants of this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,other inclusion criteria,text,,,,,,,,,Other inclusion criteria applied to the participants of this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,exclusion criteria,ontology_array,,,CatalogueOntologies,Inclusion Exclusion Criteria,,,,,Exclusion criteria applied to the participants of this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,other exclusion criteria,text,,,,,,,,,Other exclusion criteria applied to the participants of this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" +Resources,,countries,ontology_array,,,CatalogueOntologies,Countries,,,,dct: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,,,,dct: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,,,,,Which population age groups are captured in this resource? Select all that are relevant,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +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" +Resources,,other exclusion criteria,text,,,,,,,,,Other exclusion criteria applied to the participants of this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,population entry,ontology_array,,,CatalogueOntologies,Population entry,,,,,Select the possible causes / events that trigger the registration of a person in the data source,"DataCatalogueFlat,EMA,RWEStaging" Resources,,population entry other,text,,,,,,,,,"If other, specify the causes of entry to the underlying population","DataCatalogueFlat,EMA,RWEStaging" Resources,,population exit,ontology_array,,,CatalogueOntologies,Population exit,,,,,Select the possible causes / events that trigger the de-registration of a person in the data source,"DataCatalogueFlat,EMA,RWEStaging" Resources,,population exit other,text,,,,,,,,,"If other, specify the causes of exit from the underlying population","DataCatalogueFlat,EMA,RWEStaging" -Resources,,population disease,ontology_array,,,CatalogueOntologies,Diseases,,,,,Is information on a specific disease subpopulation collected (e.g. as in a disease-specific registry or cohort)?,"DataCatalogueFlat,CohortsStaging,RWEStaging" +Resources,,population disease,ontology_array,,,CatalogueOntologies,Diseases,,,,,Is information on a specific disease subpopulation collected (e.g. as in a disease-specific registry or cohort)?,"DataCatalogueFlat,CohortsStaging,RWEStaging,INTEGRATE" Resources,,population oncology topology,ontology_array,,,CatalogueOntologies,ICDO topologies,,,,,"Is information on specific cancer subtype(s) collected? If yes, select topology specifications","DataCatalogueFlat,CohortsStaging,RWEStaging" Resources,,population oncology morphology,ontology_array,,,CatalogueOntologies,ICDO morphologies,,,,,"Is information on specific cancer subtype(s) collected? If yes, select morphology specifications","DataCatalogueFlat,CohortsStaging,RWEStaging" -Resources,,population coverage,text,,,,,,,,,Estimated percentage of the population covered by the data source in the catchment area. Please describe the denominator,"DataCatalogueFlat,EMA,RWEStaging" +Resources,,population coverage,text,,,,,,,,,Estimated percentage of the population covered by the data source in the catchment area. Please describe the denominator,"DataCatalogueFlat,EMA,RWEStaging,INTEGRATE" Resources,,population not covered,text,,,,,,,,,"Description of the population covered by the data source in the catchment area whose data are not collected, where applicable (e.g. people who are registered only for private care) ","DataCatalogueFlat,EMA,RWEStaging" -Resources,,counts,refback,,,,Resource counts,,resource,,,Counts of e.g. samples defined for this resource,"DataCatalogueFlat,RWEStaging,StudiesStaging" -Resources,,contributors,heading,,,,,,,,,List of relevant collaborations,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,people involved,refback,,,,Contacts,,resource,,dcat:contactPoint,Persons involved and their role(s),"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,organisations involved,refback,,,,Organisations,,resource,,,Organisations involved and their role(s),"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts" +Resources,,counts,refback,,,,Resource counts,,resource,,,Counts of e.g. samples defined for this resource,"DataCatalogueFlat,RWEStaging,StudiesStaging,INTEGRATE" +Resources,,contributors,heading,,,,,,,,,List of relevant collaborations,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,people involved,refback,,,,Contacts,,resource,,dcat:contactPoint,Persons involved and their role(s),"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,organisations involved,refback,,,,Organisations,,resource,,,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 and samples,heading,,,,,,,,,Data model and contents,"DataCatalogueFlat,EMA,RWEStaging,CohortsStaging" @@ -89,23 +89,23 @@ Resources,,disease details other,text,,,,,,,,,Specify disease details if not pre 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" -Resources,,linkage,heading,,,,,,,,,Data linkage,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts" +Resources,,linkage,heading,,,,,,,,,Data linkage,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,has identifier,bool,,,,,,,,,Is there a unique identifier for a person in the data bank?,"DataCatalogueFlat,RWEStaging" Resources,,identifier description,text,,,,,,,,,"Describe the variable that is used as a unique identifier for a person in the data bank. If the unique identifier is not at level of a person (for example hospital encounter), describe how this is translated to an individual level","DataCatalogueFlat,RWEStaging" Resources,,prelinked,bool,,,,,,,,,Is the data from this data source linked to other data sources?,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCUCohorts" -Resources,,linkage options,text,,,,,,,,,Linkage options with additional data resources that are available for this resource,"DataCatalogueFlat,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts" +Resources,,linkage options,text,,,,,,,,,Linkage options with additional data resources that are available for this resource,"DataCatalogueFlat,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,linkage description,text,,,,,,,,,Provide a high-level description of the linkages that are currently available for this data resource,EMA -Resources,,linkage possibility,bool,,,,,,,,,Can this data source be linked to other data sources?,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCUCohorts" +Resources,,linkage possibility,bool,,,,,,,,,Can this data source be linked to other data sources?,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCUCohorts,INTEGRATE" Resources,,linkage possibility description,text,,,,,,,,,Description of data sources that can be linked to this data source,EMA Resources,,linked resources,refback,,,,Linkages,,resource,,,List of resources that are or can be linked to this main resource,"DataCatalogueFlat,EMA,RWEStaging" -Resources,,access conditions,heading,,,,,,,,,Access and validation information,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,informed consent type,ontology,,,CatalogueOntologies,Informed consent types,,,,,What type of informed consent was given for data resource?,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" +Resources,,access conditions,heading,,,,,,,,,Access and validation information,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,informed consent type,ontology,,,CatalogueOntologies,Informed consent types,,,,,What type of informed consent was given for data resource?,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,informed consent required,ontology,,,CatalogueOntologies,Informed consent required,,,,,Is informed consent required for use of the data for research purposes?,"DataCatalogueFlat,EMA,RWEStaging" Resources,,informed consent other,text,,,,,,,,,"If 'other', describe the conditions when informed consent is required","DataCatalogueFlat,EMA,RWEStaging" -Resources,,data access conditions,ontology_array,,,CatalogueOntologies,Data access conditions,,,,,Codes defining data access terms and conditions,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,data use conditions,ontology_array,,,CatalogueOntologies,Data use conditions,,,,,Codes defining data use terms and conditions,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,data access conditions description,text,,,,,,,,,Description of data access terms and use conditions,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,data access fee,bool,,,,,,,,,Does a fee apply to gain access to data of this resource?,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts" +Resources,,data access conditions,ontology_array,,,CatalogueOntologies,Data access conditions,,,,,Codes defining data access terms and conditions,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,data use conditions,ontology_array,,,CatalogueOntologies,Data use conditions,,,,,Codes defining data use terms and conditions,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,data access conditions description,text,,,,,,,,,Description of data access terms and use conditions,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,data access fee,bool,,,,,,,,,Does a fee apply to gain access to data of this resource?,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,access identifiable data,text,,,,,,,,,Can identifiable data be accessed in the data bank (including patient/practitioner name/practice name)?,"DataCatalogueFlat,RWEStaging" Resources,,access identifiable data route,text,,,,,,,,,"If yes above, what is the route to access or process this information? What permission is required?","DataCatalogueFlat,RWEStaging" Resources,,access subject details,bool,,,,,,,,,Can individual patients/practitioners/practices be contacted in the data bank?,"DataCatalogueFlat,EMA,RWEStaging" @@ -114,8 +114,8 @@ Resources,,access third party,bool,,,,,,,,,Can (an extract of) the data bank be Resources,,access third party conditions,text,,,,,,,,,"If above is 'yes', describe the conditions under which third-party access may be granted","DataCatalogueFlat,RWEStaging" Resources,,access non EU,bool,,,,,,,,,Can (an extract of) the data bank be accessed with permission by a non-EU/EEA institution?,"DataCatalogueFlat,RWEStaging" 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" -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" +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,,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" @@ -129,9 +129,9 @@ Resources,,refresh period,ontology_array,,,CatalogueOntologies,Refresh periods,, Resources,,date last refresh,date,,,,,,,,,Date of last update/refresh,"DataCatalogueFlat,EMA,RWEStaging" Resources,,preservation,bool,,,,,,,,,Are records preserved in the data bank indefinitely?,"DataCatalogueFlat,EMA,RWEStaging" Resources,,preservation duration,int,,,,,,,,,"If 'no' to the above, for how long (in years) are records preserved in the data bank?","DataCatalogueFlat,EMA,RWEStaging" -Resources,,quality,heading,,,,,,,,,List of relevant studies conducted using the data bank,"DataCatalogueFlat,EMA,RWEStaging" +Resources,,quality,heading,,,,,,,,,List of relevant studies conducted using the data bank,"DataCatalogueFlat,EMA,RWEStaging,INTEGRATE" 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" +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,,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" @@ -145,19 +145,19 @@ Resources,,quality validation methods,text,,,,,,,,,What methods or processes are Resources,,correction methods,text,,,,,,,,,What methods or processes are applied to correct illogical values in the data bank?,"DataCatalogueFlat,RWEStaging" Resources,,quality validation results,,,,,,,,,,"If available, provide a link to a publication of the data quality check and validation results","DataCatalogueFlat,RWEStaging" Resources,,quality marks,ontology_array,,,CatalogueOntologies,Study quality marks,,,,,"Quality marks, such as ENCePP seal",EMA -Resources,,standards,heading,,,,,,,,,Use of standard data models and ontologies,"DataCatalogueFlat,EMA,RWEStaging" +Resources,,standards,heading,,,,,,,,,Use of standard data models and ontologies,"DataCatalogueFlat,EMA,RWEStaging,INTEGRATE" Resources,,mappings to common data models,refback,,,,Dataset mappings,,source,,,Overview of dataset mappings available,"DataCatalogueFlat,RWEStaging" Resources,,common data models other,text,,,,,,,,,"If not in list above, give the name of cdm(s) used by this data source","DataCatalogueFlat,EMA,RWEStaging" -Resources,,ETL standard vocabularies,ontology_array,,,CatalogueOntologies,Vocabularies,,,,,"Are data mapped to standardised vocabularies during ETL to the CDM? If yes, what vocabularies are used for events, such as diagnoses?","DataCatalogueFlat,RWEStaging" -Resources,,ETL standard vocabularies other,text,,,,,,,,,"If other, what other vocabularies are used?","DataCatalogueFlat,RWEStaging" +Resources,,ETL standard vocabularies,ontology_array,,,CatalogueOntologies,Vocabularies,,,,,"Are data mapped to standardised vocabularies during ETL to the CDM? If yes, what vocabularies are used for events, such as diagnoses?","DataCatalogueFlat,RWEStaging,INTEGRATE" +Resources,,ETL standard vocabularies other,text,,,,,,,,,"If other, what other vocabularies are used?","DataCatalogueFlat,RWEStaging,INTEGRATE" Resources,,information,heading,,,,,,,,,Other information,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" Resources,,publications,refback,,,,Publications,,resource,,,Publication(s) about this resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,funding sources,ontology_array,,,CatalogueOntologies,Funding types,,,,,Specify the main financial support sources for the data source in the last three years. Select all that apply,"DataCatalogueFlat,EMA,RWEStaging" +Resources,,funding sources,ontology_array,,,CatalogueOntologies,Funding types,,,,,Specify the main financial support sources for the data source in the last three years. Select all that apply,"DataCatalogueFlat,EMA,RWEStaging,INTEGRATE" Resources,,funding scheme,ontology_array,,,CatalogueOntologies,Study funding,,,,,The source of funding for the study. Select all that apply,"DataCatalogueFlat,EMA,StudiesStaging" Resources,,funding statement,text,,,,,,,,,Statement listing funding that was obtained for this resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" Resources,,citation requirements,text,,,,,,,,,Citation regulation for this resource,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCUCohorts" Resources,,acknowledgements,text,,,,,,,,,Acknowledgement statement and citation regulation for this resource,"DataCatalogueFlat,CohortsStaging,RWEStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" -Resources,,documentation,refback,,,,Documentation,,resource,,,"Descriptive document(s) available for this resource, e.g. informed consent","DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts" +Resources,,documentation,refback,,,,Documentation,,resource,,,"Descriptive document(s) available for this resource, e.g. informed consent","DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,supplementary information,text,,,,,,,,,Any other information that needs to be disclosed for this resource,"DataCatalogueFlat,CohortsStaging,RWEStaging" Resources,,study details,heading,,,,,,,,,List of relevant collaborations,"DataCatalogueFlat,EMA,StudiesStaging" Resources,,study requirements,ontology_array,,,CatalogueOntologies,Study requirements,,,,,Study requirements,EMA diff --git a/data/_models/shared/Subpopulations.csv b/data/_models/shared/Subpopulations.csv index adc4f24ede..bde936b154 100644 --- a/data/_models/shared/Subpopulations.csv +++ b/data/_models/shared/Subpopulations.csv @@ -1,18 +1,18 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles,visible -Subpopulations,,,,,,,,,,,dcat:Dataset,Subpopulations defined for this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts", -Subpopulations,,resource,ref,1,TRUE,,Resources,,,,dcterms:isPartOf,Resource this subpopulation is part of,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts", -Subpopulations,,name,,1,TRUE,,,,,,dcterms:title,"Subpopulation name, e.g. 'mothers in first trimester','newborns'","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts", -Subpopulations,,description,text,,,,,,,,dcterms:description,Subpopulation description,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts", -Subpopulations,,number of participants,int,,,,,,,,,Number of participants in this subpopulation,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", +Subpopulations,,,,,,,,,,,dcat:Dataset,Subpopulations defined for this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,resource,ref,1,TRUE,,Resources,,,,dcterms:isPartOf,Resource this subpopulation is part of,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,name,,1,TRUE,,,,,,dcterms:title,"Subpopulation name, e.g. 'mothers in first trimester','newborns'","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,description,text,,,,,,,,dcterms:description,Subpopulation description,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,number of participants,int,,,,,,,,,Number of participants in this subpopulation,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", Subpopulations,,counts,refback,,,,Subpopulation counts,,subpopulation,,,"Total number of unique individuals per age(group), gender and year","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", -Subpopulations,,inclusion start,int,,,,,,,,dcat:startDate,Year of first included participant,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", -Subpopulations,,inclusion end,int,,,,,,,,dcat:endDate,Year of last included participant. Leave empty if data collection is ongoing,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", -Subpopulations,,age groups,ontology_array,,,CatalogueOntologies,Age groups,,,,,Age groups within this subpopulation,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", -Subpopulations,,main medical condition,ontology_array,,,CatalogueOntologies,Diseases,,,,dcat:theme,"Disease groups within this subpopulation, based on ICD-10 and ORPHA code classifications","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", -Subpopulations,,comorbidity,ontology_array,,,CatalogueOntologies,Diseases,,,,,"Comorbidity within this subpopulation, based on ICD-10 classification","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", -Subpopulations,,countries,ontology_array,,,CatalogueOntologies,Countries,,,,dcterms:coverage,Countries where data from this subpopulation largely originate from,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", -Subpopulations,,regions,ontology_array,,,CatalogueOntologies,Regions,,,,dcterms:coverage,Geographical regions where data from this subpopulation largely originate from,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", -Subpopulations,,inclusion criteria,ontology_array,,,CatalogueOntologies,Inclusion Exclusion Criteria,,,,,Inclusion criteria applied to this subpopulation,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", -Subpopulations,,other inclusion criteria,text,,,,,,,,,Other inclusion criteria applied to this subpopulation,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", -Subpopulations,,exclusion criteria,ontology_array,,,CatalogueOntologies,Inclusion Exclusion Criteria,,,,,Exclusion criteria applied to this subpopulation,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", -Subpopulations,,other exclusion criteria,text,,,,,,,,,Other exclusion criteria applied to this subpopulation,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts", +Subpopulations,,inclusion start,int,,,,,,,,dcat:startDate,Year of first included participant,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,inclusion end,int,,,,,,,,dcat:endDate,Year of last included participant. Leave empty if data collection is ongoing,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,age groups,ontology_array,,,CatalogueOntologies,Age groups,,,,,Age groups within this subpopulation,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,main medical condition,ontology_array,,,CatalogueOntologies,Diseases,,,,dcat:theme,"Disease groups within this subpopulation, based on ICD-10 and ORPHA code classifications","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,comorbidity,ontology_array,,,CatalogueOntologies,Diseases,,,,,"Comorbidity within this subpopulation, based on ICD-10 classification","DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,countries,ontology_array,,,CatalogueOntologies,Countries,,,,dcterms:coverage,Countries where data from this subpopulation largely originate from,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,regions,ontology_array,,,CatalogueOntologies,Regions,,,,dcterms:coverage,Geographical regions where data from this subpopulation largely originate from,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,inclusion criteria,ontology_array,,,CatalogueOntologies,Inclusion Exclusion Criteria,,,,,Inclusion criteria applied to this subpopulation,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,other inclusion criteria,text,,,,,,,,,Other inclusion criteria applied to this subpopulation,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,exclusion criteria,ontology_array,,,CatalogueOntologies,Inclusion Exclusion Criteria,,,,,Exclusion criteria applied to this subpopulation,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", +Subpopulations,,other exclusion criteria,text,,,,,,,,,Other exclusion criteria applied to this subpopulation,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE", diff --git a/data/_models/shared/Version.csv b/data/_models/shared/Version.csv index a96a5c6d13..bec17c4255 100644 --- a/data/_models/shared/Version.csv +++ b/data/_models/shared/Version.csv @@ -1,2 +1,2 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles,visible -Version,,,,,,,,,,,,5.4,"DataCatalogueFlat,EMA,RWEStaging,CohortsStaging,StudiesStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts", +Version,,,,,,,,,,,,5.4,"DataCatalogueFlat,EMA,RWEStaging,CohortsStaging,StudiesStaging,UMCGCohortsStaging,NetworksStaging,UMCUCohorts,INTEGRATE", diff --git a/data/_profiles/INTEGRATECohorts.yaml b/data/_profiles/INTEGRATECohorts.yaml new file mode 100644 index 0000000000..bd0cb6d110 --- /dev/null +++ b/data/_profiles/INTEGRATECohorts.yaml @@ -0,0 +1,18 @@ +--- +name: INTEGRATECohorts + +description: Staging area for filling out INTEGRATE cohort metadata + +profileTags: INTEGRATE + +demoData: _demodata/applications/datacatalogue_cohortstaging + +settings: + +# special options +ontologiesToFixedSchema: CatalogueOntologies +setFixedSchemaViewPermission: anonymous +firstCreateSchemasIfMissing: + - name: catalogue + profile: _profiles/DataCatalogue.yaml + importDemoData: false