feat/miabis_biobanks

Author: svituz

data/example-rdf/turtle/biobank.ttl

@@ -6,7 +6,6 @@
 @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 obo: <http://purl.obolibrary.org/obo/> .
 @prefix vcard: <http://www.w3.org/2006/vcard/ns#> .
@@ -15,10 +14,9 @@
 
 
 :collection
-  a obo:OBIB_0000645, dcat:Dataset;
+  a obo:OBIB_0000616, dcat:Dataset;
   dct:identifier "collection-id";
-  dct:isPartOf :catalog;
-  obo:BFO_0000050 :biobank;
+  obo:OBIB_0000735 :biobank;
   dct:title "Muscle tissue collection";
   dcat:contactPoint [ a vcard:Individual;
       vcard:email <mailto:info@ejprdbiobank.org>;
@@ -27,10 +25,7 @@
       vcard:hasHonorificSuffix "PhD"
     ];
   dct:description "Example collection of samples";
-  dcat:theme ordo:Orphanet_589;
-  fdp-o:metadataIdentifier [ a datacite:Identifier;
-      dct:identifier :collection
-    ] .
+  dcat:theme ordo:Orphanet_589 .
 
 :biobank
   a obo:OBIB_0000616, dcat:Resource;
@@ -39,20 +34,16 @@
   dct:alternative "BRD";
   dct:description "Biobank with collections of biopsies of muscular diseases";
   dcat:landingPage <https://examplebiobank.org>;
-  obo:OBIB_0000735 :biobankOrganization;
+  dct:publisher :biobankOrganization;
   dct:spatial  <http://publications.europa.eu/resource/authority/country/AUT>;;
   dcat:contactPoint [ a vcard:Individual;
       vcard:email <mailto:director@ejprdbiobank.org>;
       vcard:hasGivenName "Mario";
       vcard:hasFamilyName "Rossi";
       vcard:hasHonorificSuffix "PhD"
     ];
-  obo:BFO_0000051 :collection;
-  fdp-o:metadataIdentifier [ a datacite:Identifier;
-      dct:identifier :biobank
-  ] .
+  obo:OBIB_0000732 :collection .
 
 :biobankOrganization 
-  a obo:OBIB_0000623, foaf:Organization;
-  foaf:name "University of Muscle Diseases";
-  obo:OBIB_0000732 :biobank .
+  a foaf:Organization;
+  foaf:name "University of Muscle Diseases" .

docs/biobank.md

@@ -30,7 +30,6 @@ These two concepts of MIABIS have been mapped to DCAT:Resources and denoted usin
 @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 obo: <http://purl.obolibrary.org/obo/> .
 @prefix vcard: <http://www.w3.org/2006/vcard/ns#> .
@@ -39,10 +38,9 @@ These two concepts of MIABIS have been mapped to DCAT:Resources and denoted usin
 
 
 :collection
-  a obo:OBIB_0000645, dcat:Dataset;
+  a obo:OBIB_0000616, dcat:Dataset;
   dct:identifier "collection-id";
-  dct:isPartOf :catalog;
-  obo:BFO_0000050 :biobank;
+  obo:OBIB_0000735 :biobank;
   dct:title "Muscle tissue collection";
   dcat:contactPoint [ a vcard:Individual;
       vcard:email <mailto:info@ejprdbiobank.org>;
@@ -51,10 +49,7 @@ These two concepts of MIABIS have been mapped to DCAT:Resources and denoted usin
       vcard:hasHonorificSuffix "PhD"
     ];
   dct:description "Example collection of samples";
-  dcat:theme ordo:Orphanet_589;
-  fdp-o:metadataIdentifier [ a datacite:Identifier;
-      dct:identifier :collection
-    ] .
+  dcat:theme ordo:Orphanet_589 .
 
 :biobank
   a obo:OBIB_0000616, dcat:Resource;
@@ -63,95 +58,16 @@ These two concepts of MIABIS have been mapped to DCAT:Resources and denoted usin
   dct:alternative "BRD";
   dct:description "Biobank with collections of biopsies of muscular diseases";
   dcat:landingPage <https://examplebiobank.org>;
-  obo:OBIB_0000735 :biobankOrganization;
+  dct:publisher :biobankOrganization;
   dct:spatial  <http://publications.europa.eu/resource/authority/country/AUT>;;
   dcat:contactPoint [ a vcard:Individual;
       vcard:email <mailto:director@ejprdbiobank.org>;
       vcard:hasGivenName "Mario";
       vcard:hasFamilyName "Rossi";
       vcard:hasHonorificSuffix "PhD"
     ];
-  obo:BFO_0000051 :collection;
-  fdp-o:metadataIdentifier [ a datacite:Identifier;
-      dct:identifier :biobank
-  ] .
+  obo:OBIB_0000732 :collection .
 
 :biobankOrganization 
-  a obo:OBIB_0000623, foaf:Organization;
-  foaf:name "University of Mus
-```
-
-***
-
-### Validation artifacts 
-
-##### ShEx figure
-
-<p align="center"> 
-    <a href="../images/shex/biobank.svg" target="_blank">
-        <img src="../images/shex/biobank.svg"> 
-    </a>
-</p>
-
-***
-##### ShEx
-
-``` ShEx
-PREFIX : <http://purl.org/ejp-rd/metadata-model/v1/shex/>
-PREFIX dcat:  <http://www.w3.org/ns/dcat#>
-PREFIX dct:   <http://purl.org/dc/terms/>
-PREFIX ejprd:   <http://purl.org/ejp-rd/vocabulary/>
-PREFIX foaf:  <http://xmlns.com/foaf/0.1/>
-PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
-PREFIX sio:  <http://semanticscience.org/resource/>
-PREFIX rdfs:  <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX odrl: <https://www.w3.org/TR/odrl-model/>
-PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-PREFIX obo: <http://purl.obolibrary.org/obo/>
-PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
-PREFIX datacite: <http://purl.org/spar/datacite/> 
-
-# Collection in MIABIS 2.0 represents a set of samples with at least one common characteristic (
-:collectionShape IRI {
-  rdf:type [dcat:Resource dcat:Dataset obo:OBIB_0000625]; # obo:OBIB_0000625 is "Hosted Study Collection"
-  dct:identifier xsd:string;
-  dct:title xsd:string;
-  dct:alternative xsd:string*;
-  dct:description xsd:string*;
-  dcat:theme IRI+;  # theme is used for the diseases in the collection expressed using ORDO
-  dcat:keyword xsd:string*;
-  dct:publisher [foaf:Agent];
-  dcat:landingPage IRI*;
-  dct:language xsd:string+;
-  dct:contactPoint [vcard:Individual];
-  obo:BFO_0000050 @:biobankShape # obo:BFO_0000050 is "part of"
-  # missing mapping of some properties that are present in MIABIS:
-  # age low
-  # age high
-  # age unit
-  # data categories
-  # material type
-  # storage temperature
-  # collection type
-}
-
-# In MIABIS, Biobank is defined as an organization or an organizational unit that stores samples and data related to the samples.
-# Only Organizational property are used to describe a Biobank
-:biobankShape IRI {
-  rdf:type [dcat:Resource obo:OBIB_0000616]; # obo:OBIB_0000616 is Biobank
-  dct:identifier xsd:string;
-  dct:title xsd:string;
-  dct:alternative xsd:string*;
-  dct:description xsd:stirng*;
-  dcat:landingPage IRI*;
-  obo:OBIB_0000735 :biobankOrganizationShape; # obo:OBIB_0000735 is "owned by"
-  dct:spatial IRI*;
-  dcat:contactPoint [vcard:Individual];
-  obo:BFO_0000051 @:collectionShape+; # obo:BFO_0000051 is "has part"
-}
-
-:biobankOrganizationShape IRI {
-  rdf:type [foaf:Organization obo:OBIB_0000623]; # obo:OBIB_0000623 is Biobank Organization
-  obo:OBIB_0000732 @:biobankShape # OBIB_0000732 is "owns"
-}
-```
+  a foaf:Organization;
+  foaf:name "University of Muscle Diseases" .```