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

data/_models/shared/Resource counts.csv

@@ -5,7 +5,11 @@ Resource counts,,age group,ontology,1,,CatalogueOntologies,Age groups,,,,,Select
 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,,number of samples,int,,,,,,,,,Total number of samples included in this resource,"DataCatalogueFlat,CohortsStaging",
+Resource counts,,sample type,ontology_array,,,CatalogueOntologies,BiospecimenType,,,,,Do the counts relate to one or more types of sample?,"DataCatalogueFlat,CohortsStaging",
+Resource counts,,population diseases,ontology_array,,,CatalogueOntologies,Diseases,,,,,Do the counts relate to one or more medical conditions?,"DataCatalogueFlat,CohortsStaging,RWEStaging",
 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,INTEGRATE",
+Resource counts,,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",
 Resource counts,,proportion female,int,,,,,,,,,Proportion of females in the data source,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,INTEGRATE",

data/_models/shared/Resource qualities.csv

@@ -0,0 +1,8 @@
+tableName,tableExtends,tableType,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,refLabel,defaultValue,validation,visible,computed,semantics,profiles,label,description
+Resource qualities,,,,,,,,,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Quality information, i.e. standards, assessments and certifications relating to a resource or sample collection"
+Resource qualities,,,resource,ref,1,TRUE,,Resources,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Resource the quality information pertains to"
+Resource qualities,,,quality standard,ontology,1,TRUE,CatalogueOntologies,Quality standards,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Quality standard"
+Resource qualities,,,assessment level,ontology,,TRUE,CatalogueOntologies,Assessment levels,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Assessment level"
+Resource qualities,,,certification number,,,FALSE,,,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Certification Number"
+Resource qualities,,,certification report,hyperlink,,FALSE,,,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Certification Report"
+Resource qualities,,,certification image url,hyperlink,,FALSE,,,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Certification Image"

data/_models/shared/Resources.csv

@@ -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"
 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"
@@ -50,6 +51,7 @@ 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"
 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"
@@ -72,6 +74,9 @@ Resources,,publisher,ref,,,,Organisations,,,,http://purl.org/dc/terms/publisher,
 Resources,,creator,ref_array,,,,Organisations,,,,http://purl.org/dc/terms/creator,This attribute is read only and written during migration of data from staging areas and used to produce valid dcat output. Organisation(s) that created this resource,DataCatalogueFlat
 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"
 Resources,,available data and samples,heading,,,,,,,,,Data model and contents,"DataCatalogueFlat,EMA,RWEStaging,CohortsStaging"
 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"
@@ -91,6 +96,11 @@ 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"
+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"
@@ -121,6 +131,8 @@ 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"
@@ -138,6 +150,7 @@ 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"

data/_ontologies/Assessment levels.csv

@@ -0,0 +1,3 @@
+order,name,label,parent,codesystem,code,ontologyTermURI,definition
+,eric,BBMRI-ERIC audited,,,,,
+,accredited,Accredited/Certified by accredited body,,,,,