From 082a5003e23eb27c03babd1c2fe954779c78041a Mon Sep 17 00:00:00 2001 From: Vittorio Meloni Date: Mon, 8 May 2023 11:48:14 +0200 Subject: [PATCH 01/12] feat: change of biobank resource to map MIABIS concepts --- images/shex/biobank.svg | 76 ++++++++++++++++++++++++++--------------- shapes/biobank.shex | 27 +++++---------- 2 files changed, 57 insertions(+), 46 deletions(-) diff --git a/images/shex/biobank.svg b/images/shex/biobank.svg index 0b18ff6..f62123a 100644 --- a/images/shex/biobank.svg +++ b/images/shex/biobank.svg @@ -1,68 +1,88 @@ -:biobankShapeIRIa: [ejp:Biobank]dct:title:xsd:stringdct:description:xsd:string*dcat:theme: IRI +foaf:page: IRI *:locationShapeIRIa: [dct:Location]dct:title:xsd:stringdct:description:xsd:string*:organisationShapeIRIa: [foaf:Organisation]dct:title:xsd:stringdct:description:xsd:string*foaf:page: IRI *:populationCoverageShapeIRIa: [sio:SIO_001166]rdfs:label: [ National International Regional ]dct:spatialejp:populationCoverage*dct:publisherGenerated byrdfshape:collectionShapeIRIa: [dcat:Resourcedcat:Datasetobo:OBIB_0000625]dct:title:xsd:stringdct:alternative:xsd:string*dct:description:xsd:string*dcat:theme: IRI +dcat:keyword:xsd:string*dct:publisher: [foaf:Agent]dcat:landingPage: IRI *dct:language:xsd:string+dct:contactPoint: [vcard:Individual]:biobankShapeIRIa: [dcat:Resourceobo:OBIB_0000616]dct:identifier:xsd:stringdct:title:xsd:stringdct:alternative:xsd:string*dct:description:xsd:stirng*dcat:landingPage: IRI *obo:OBIB_0000735::biobankOrganizationShapedct:spatial::locationShapedcat:contactPoint: [vcard:Individual]:biobankOrganizationShapeIRIa: [foaf:Organizationobo:OBIB_0000623]:locationShapeIRIa: [dct:Location]dct:title:xsd:stringdct:description:xsd:string*obo:OBIB_0000732obo:BFO_0000051+obo:BFO_0000050dct:spatialGenerated byrdfshape:collectionShapeIRIa: [dcat:Resourcedcat:Datasetobo:OBIB_0000625]dct:title:xsd:stringdct:alternative:xsd:string*dct:description:xsd:string*dcat:theme: IRI +dcat:keyword:xsd:string*dct:publisher: [foaf:Agent]dcat:landingPage: IRI *dct:language:xsd:string+dct:contactPoint: [vcard:Individual]:biobankShapeIRIa: [dcat:Resourceobo:OBIB_0000616]dct:identifier:xsd:stringdct:title:xsd:stringdct:alternative:xsd:string*dct:description:xsd:stirng*dcat:landingPage: IRI *obo:OBIB_0000735::biobankOrganizationShapedct:spatial::locationShapedcat:contactPoint: [vcard:Individual]:biobankOrganizationShapeIRIa: [foaf:Organizationobo:OBIB_0000623]:locationShapeIRIa: [dct:Location]dct:title:xsd:stringdct:description:xsd:string*obo:OBIB_0000732obo:BFO_0000051+obo:BFO_0000050dct:spatialGenerated byrdfshape:collectionShapeIRIa: [dcat:Resourcedcat:Datasetobo:OBIB_0000625]dct:identifier:xsd:stringdct:title:xsd:stringdct:alternative:xsd:string*dct:description:xsd:string*dcat:theme: IRI +dcat:keyword:xsd:string*dct:publisher: [foaf:Agent]dcat:landingPage: IRI *dct:language:xsd:string+dct:contactPoint: [vcard:Individual]:biobankShapeIRIa: [dcat:Resourceobo:OBIB_0000616]dct:identifier:xsd:stringdct:title:xsd:stringdct:alternative:xsd:string*dct:description:xsd:stirng*dcat:landingPage: IRI *obo:OBIB_0000735::biobankOrganizationShapedct:spatial: IRI *dcat:contactPoint: [vcard:Individual]:biobankOrganizationShapeIRIa: [foaf:Organizationobo:OBIB_0000623]obo:OBIB_0000732obo:BFO_0000051+obo:BFO_0000050Generated byrdfshape:collectionShapeIRIa: [dcat:Resourcedcat:Datasetobo:OBIB_0000625]dct:identifier:xsd:stringdct:title:xsd:stringdct:alternative:xsd:string*dct:description:xsd:string*dcat:theme: IRI +dcat:keyword:xsd:string*dct:publisher: [foaf:Agent]dcat:landingPage: IRI *dct:language:xsd:string+dct:contactPoint: [vcard:Individual]:biobankShapeIRIa: [dcat:Resourceobo:OBIB_0000616]dct:identifier:xsd:stringdct:title:xsd:stringdct:alternative:xsd:string*dct:description:xsd:stirng*dcat:landingPage: IRI *obo:OBIB_0000735::biobankOrganizationShapedct:spatial: IRI *dcat:contactPoint: [vcard:Individual]:biobankOrganizationShapeIRIa: [foaf:Organizationobo:OBIB_0000623]obo:OBIB_0000732obo:BFO_0000051+obo:BFO_0000050Generated byrdfshape:biobankShapeIRIa: [ejp:Biobank]dct:title:xsd:stringdct:description:xsd:string*dcat:theme: IRI +foaf:page: IRI *:locationShapeIRIa: [dct:Location]dct:title:xsd:stringdct:description:xsd:string*:organisationShapeIRIa: [foaf:Organisation]dct:title:xsd:stringdct:description:xsd:string*foaf:page: IRI *:populationCoverageShapeIRIa: [sio:SIO_001166]rdfs:label: [ National International Regional ]dct:spatialejp:populationCoverage*dct:publisherGenerated byrdfshape \ No newline at end of file diff --git a/shapes/biobank.shex b/shapes/biobank.shex index cfdb0cf..60f015b 100644 --- a/shapes/biobank.shex +++ b/shapes/biobank.shex @@ -62,4 +62,4 @@ PREFIX datacite: :biobankOrganizationShape IRI { rdf:type [foaf:Organization obo:OBIB_0000623]; # obo:OBIB_0000623 is Biobank Organization obo:OBIB_0000732 @:biobankShape # OBIB_0000732 is "owns" -} \ No newline at end of file +}git \ No newline at end of file From 95b30e3711565ffb877c7815a1e1018f1c0e075e Mon Sep 17 00:00:00 2001 From: Vittorio Meloni Date: Mon, 8 May 2023 12:12:51 +0200 Subject: [PATCH 05/12] feat: changes example for biobank --- images/shex/biobank.svg | 68 ----------------------------------------- shapes/biobank.shex | 2 +- 2 files changed, 1 insertion(+), 69 deletions(-) diff --git a/images/shex/biobank.svg b/images/shex/biobank.svg index ee2d16d..b294ad5 100644 --- a/images/shex/biobank.svg +++ b/images/shex/biobank.svg @@ -1,71 +1,3 @@ -:biobankShapeIRIa: [ejp:Biobank]dct:title:xsd:stringdct:description:xsd:string*dcat:theme: IRI +foaf:page: IRI *:locationShapeIRIa: [dct:Location]dct:title:xsd:stringdct:description:xsd:string*:organisationShapeIRIa: [foaf:Organisation]dct:title:xsd:stringdct:description:xsd:string*foaf:page: IRI *:populationCoverageShapeIRIa: [sio:SIO_001166]rdfs:label: [ National International Regional ]dct:spatialejp:populationCoverage*dct:publisherGenerated byrdfshape:collectionShapeIRIa:dcat:Dataseta:obo:OBIB_0000616dct:identifier:xsd:stringdct:title:xsd:stringfoaf:logo: IRI ?dct:description:xsd:string*dct:alternative:xsd:string*dct:license: IRIdcat:theme: IRI +dcat:keyword:xsd:string*dcat:landingPage: IRI *dct:language:xsd:string+ejprd:populationCoverage: [ National International Regional European ]ejprd:personalData:xsd:string?ejprd:vpConnection: [ejprd:VPDiscoverableejprd:VPContentDiscovery]dct:accessRights: IRI ?odrl:hasPolicy: IRI ?dct:conformsTo: IRI ?dct:contactPoint:vcard:Kind?:biobankShapeIRIa:foaf:Organizationa:obo:OBIB_0000623dct:identifier:xsd:stringdct:title:xsd:stringdct:alternative:xsd:string*dct:description:xsd:stirng*dcat:landingPage: IRI *dcat:contactPoint:vcard:Kind:biobankLegalEntityIRIa: [obo:OMRSE_00000038]dct:title:xsd:string:locationShapeIRIa: [dct:Location]dct:title:xsd:stringdct:description:xsd:string*dct:spatialobo:RO_0000053obo:OBIB_0000732+dct:publisherGenerated byrdfshape \ No newline at end of file diff --git a/shapes/biobank.shex b/shapes/biobank.shex index f69ae44..772012b 100644 --- a/shapes/biobank.shex +++ b/shapes/biobank.shex @@ -14,7 +14,8 @@ PREFIX datacite: # Collection in MIABIS 2.0 represents a collection as a set of samples with at least one common characteristic :collectionShape IRI { - rdf:type [dcat:Resource obo:OBIB_0000616]; # obo:OBIB_0000616 is "Biobank" + rdf:type dcat:Dataset; + rdf:type obo:OBIB_0000616; # obo:OBIB_0000616 is "Biobank" dct:identifier xsd:string; dct:title xsd:string; foaf:logo IRI?; @@ -23,7 +24,7 @@ PREFIX datacite: dct:license IRI; dcat:theme IRI+; dcat:keyword xsd:string*; - dct:publisher @:biobankShape # obo:OBIB_0000735 is "is owned by", reverse of OBIB_0000732 "owns" + dct:publisher @:biobankShape; dcat:landingPage IRI*; dct:language xsd:string+; ejprd:populationCoverage ["National" "International" "Regional" "European"]; @@ -32,31 +33,32 @@ PREFIX datacite: dct:accessRights IRI?; odrl:hasPolicy IRI?; dct:conformsTo IRI?; - dct:contactPoint [vcard:Individual]?; -} - -:locationShape IRI { - a [dct:Location]; - dct:title xsd:string; - dct:description xsd:string*; + dct:contactPoint vcard:Kind? } # 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 [foaf:Organization obo:OBIB_0000623]; # obo:OBIB_0000623 is Biobank Organization + rdf:type foaf:Organization; + rdf:type obo:OBIB_0000623; # obo:OBIB_0000623 is Biobank Organization dct:identifier xsd:string; dct:title xsd:string; dct:alternative xsd:string*; dct:description xsd:stirng*; dcat:landingPage IRI*; dct:spatial @:locationShape; - dcat:contactPoint [vcard:Individual]; - obo:OBIB_0000732 @:collectionShape+; # OBIB_0000732 is "owns" - obo:RO_0000053 @:biobankLegalEntity # + dcat:contactPoint vcard:Kind; + obo:RO_0000053 @:biobankLegalEntity; # obo:RO_0000053 is a generic "has characteristic" that MUST have "Legal entity" as object + obo:OBIB_0000732 @:collectionShape+ # OBIB_0000732 is "owns" } :biobankLegalEntity IRI { rdf:type [obo:OMRSE_00000038]; # OMRSE_00000038 is legal person role dct:title xsd:string } + +:locationShape IRI { + a [dct:Location]; + dct:title xsd:string; + dct:description xsd:string*; +} \ No newline at end of file From 190e6027a34d992709cc454e4a441ed7c85a4b3c Mon Sep 17 00:00:00 2001 From: Vittorio Meloni Date: Fri, 15 Sep 2023 13:54:33 +0200 Subject: [PATCH 12/12] feat: removes dct:alternative and other minor changes --- data/example-rdf/turtle/biobank.ttl | 6 ++---- docs/biobank.md | 9 ++++----- images/shex/biobank.svg | 30 +++++++++++++---------------- shapes/biobank.shex | 10 ++++------ 4 files changed, 23 insertions(+), 32 deletions(-) diff --git a/data/example-rdf/turtle/biobank.ttl b/data/example-rdf/turtle/biobank.ttl index 2c458e1..5e2260b 100644 --- a/data/example-rdf/turtle/biobank.ttl +++ b/data/example-rdf/turtle/biobank.ttl @@ -14,11 +14,10 @@ :collection - a obo:OBIB_0000616, dcat:Resouce; + a obo:OBIB_0000616, dcat:Resource; dct:identifier "collection-id"; dct:title "Muscle Tissue Collection"; dct:description "Example collection of samples"; - dct:alternative "MTC"; dcat:theme ordo:Orphanet_589; dcat:keyword "Myastenia gravis" dct:publisher :biobank; @@ -36,9 +35,8 @@ a obo:OBIB_0000623, foaf:Organization; dct:identifier "biobank-id"; dct:title "Biobank of Rare Diseases"; - dct:alternative "BRD"; dct:description "Biobank with collections of biopsies of muscular diseases"; - dcat:landingPage ; + fofa:homepage ; dct:spatial ;; obo:RO_0000053 :biobankOrganization; # has characteristic. The object MUST be of type Legal en obo:OBIB_0000732 :collection . diff --git a/docs/biobank.md b/docs/biobank.md index 438bfce..0ec276b 100644 --- a/docs/biobank.md +++ b/docs/biobank.md @@ -39,11 +39,10 @@ These two concepts of MIABIS have been modelled similarly to Dataset and denoted :collection - a obo:OBIB_0000616, dcat:Resouce; + a obo:OBIB_0000616, dcat:Resource; dct:identifier "collection-id"; dct:title "Muscle Tissue Collection"; dct:description "Example collection of samples"; - dct:alternative "MTC"; dcat:theme ordo:Orphanet_589; dcat:keyword "Myastenia gravis" dct:publisher :biobank; @@ -61,9 +60,8 @@ These two concepts of MIABIS have been modelled similarly to Dataset and denoted a obo:OBIB_0000623, foaf:Organization; dct:identifier "biobank-id"; dct:title "Biobank of Rare Diseases"; - dct:alternative "BRD"; dct:description "Biobank with collections of biopsies of muscular diseases"; - dcat:landingPage ; + fofa:homepage ; dct:spatial ;; obo:RO_0000053 :biobankOrganization; # has characteristic. The object MUST be of type Legal en obo:OBIB_0000732 :collection . @@ -74,4 +72,5 @@ These two concepts of MIABIS have been modelled similarly to Dataset and denoted :biobankOrganization a obo:OMRSE_00000038; - foaf:name "University of Muscle Diseases" .`` + foaf:name "University of Muscle Diseases" . +``` diff --git a/images/shex/biobank.svg b/images/shex/biobank.svg index 350fd6d..807b031 100644 --- a/images/shex/biobank.svg +++ b/images/shex/biobank.svg @@ -1,17 +1,17 @@ -:collectionShapeIRIa:dcat:Dataseta:obo:OBIB_0000616dct:identifier:xsd:stringdct:title:xsd:stringfoaf:logo: IRI ?dct:description:xsd:string*dct:alternative:xsd:string*dct:license: IRIdcat:theme: IRI +dcat:keyword:xsd:string*dcat:landingPage: IRI *dct:language:xsd:string+ejprd:populationCoverage: [ National International Regional European ]ejprd:personalData:xsd:string?ejprd:vpConnection: [ejprd:VPDiscoverableejprd:VPContentDiscovery]dct:accessRights: IRI ?odrl:hasPolicy: IRI ?dct:conformsTo: IRI ?dct:contactPoint:vcard:Kind?:biobankShapeIRIa:foaf:Organizationa:obo:OBIB_0000623dct:identifier:xsd:stringdct:title:xsd:stringdct:alternative:xsd:string*dct:description:xsd:stirng*dcat:landingPage: IRI *dcat:contactPoint:vcard:Kind:biobankLegalEntityIRIa: [obo:OMRSE_00000038]dct:title:xsd:string:locationShapeIRIa: [dct:Location]dct:title:xsd:stringdct:description:xsd:string*dct:spatialobo:RO_0000053obo:OBIB_0000732+dct:publisherGenerated byrdfshape:collectionShapeIRIa:dcat:Resourcea:obo:OBIB_0000616dct:identifier:xsd:stringdct:title:xsd:stringfoaf:logo: IRI ?dct:description:xsd:string*dct:license: IRIdcat:theme: IRI +dcat:keyword:xsd:string*dcat:landingPage: IRI *dct:language:xsd:string+ejprd:populationCoverage: [ National International Regional European ]ejprd:personalData:xsd:string?ejprd:vpConnection: [ejprd:VPDiscoverableejprd:VPContentDiscovery]dct:accessRights: IRI ?odrl:hasPolicy: IRI ?dct:conformsTo: IRI ?dct:contactPoint:vcard:Kind?:biobankShapeIRIa:foaf:Organizationa:obo:OBIB_0000623dct:identifier:xsd:stringdct:title:xsd:stringdct:description:xsd:string*foaf:homepage: IRI *dcat:contactPoint:vcard:Kind:biobankLegalEntityIRIa: [obo:OMRSE_00000038]dct:title:xsd:string:locationShapeIRIa: [dct:Location]dct:title:xsd:stringdct:description:xsd:string*dct:spatialobo:RO_0000053?obo:OBIB_0000732+dct:publisherGenerated byrdfshape