molgenis / molgenis

MOLGENIS - for scientific data: management, exploration, integration and analysis.
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Feat/fair update to support fdp spec #9402

Closed svituz closed 1 year ago

svituz commented 1 year ago

This PR changes the FAIR module to support the new specification of the FDP. It changes both the FDP.xlsx template and the source code. In the EMX file, some tags have been deleted (e.g., the ones from r3d ontology) or replaced and some others have been added (e.g. some fdp-o specific terms such as fdp-o:MetadataService). Also, in the model two attributes have been added to the FDP entities (Metadata, Catalog, Dataset and Distribution):

The code has been changed to create the LDP DirectContainer resource that contains the navigation information for FDP Resource

An example of the resulting turtle is

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix lang: <http://id.loc.gov/vocabulary/iso639-1/> .
@prefix fdp-o: <https://w3id.org/fdp/fdp-o#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix orcid: <http://orcid.org/> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix datacite: <http://purl.org/spar/datacite/> .
@prefix mlga: <http://molgenis.org/audit/> .
@prefix ldp: <http://www.w3.org/ns/ldp#> .

<https://localhost/api/fdp> a dcat:Resource, dcat:DataService, fdp-o:FAIRDataPoint,
    fdp-o:MetadataService;
  dct:title "Test FDP";
  rdfs:label "Test FDP";
  dct:hasVersion "1.0.0";
  dct:description "FDP exposing test metadata";
  dct:publisher [ a foaf:Agent;
      foaf:name "FDP publisher"
    ];
  dct:language <http://lexvo.org/id/iso639-3/eng>;
  dct:conformsTo "FAIR Data Point Profile";
  dct:rights [ a dct:RightsStatement;
      dct:description "This resource has no access restriction"
    ];
  fdp-o:metadataIssued "2021-01-27T00:00:00Z"^^xsd:dateTime;
  fdp-o:metadataModified "2022-12-15T00:00:00Z"^^xsd:dateTime;
  fdp-o:startDate "2021-01-27T00:00:00Z"^^xsd:dateTime;
  fdp-o:softwareVersion "10.1.0-SNAPSHOT";
  fdp-o:metadataCatalog <http://localhost/api/fdp/fdp_Catalog/catalog>;
  fdp-o:metadataIdentifier [ a datacite:Identifier;
      dct:identifier <https://locahost/api/fdp>
    ] .

<https://localhost/api/fdp/dc> a ldp:DirectContainer;
  dct:title "Catalogs";
  ldp:membershipResource <https://localhost/api/fdp>;
  ldp:hasMemberRelation fdp-o:metadataCatalog;
  ldp:contains <http://localhost/api/fdp/fdp_Catalog/catalog> .

Checklist

sonarcloud[bot] commented 1 year ago

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 1 Code Smell

82.1% 82.1% Coverage
0.0% 0.0% Duplication