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Adding skos-xref-duplicate to obo compliance suite #752

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May 9, 2024
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Adding skos-xref-duplicate to obo compliance suite #752

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df13302
Adding skos-xref-duplicate to obo compliance suite
cmungall May 7, 2024
29e1ec7
derived files
cmungall May 7, 2024
84abd6e
Merge branch 'main' into obographs-issue-102
cmungall May 8, 2024
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15 changes: 15 additions & 0 deletions tests/input/obo-compliance.obo
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Expand Up @@ -268,6 +268,21 @@ relationship: skos:exactMatch Y:1
id: skos:exactMatch
is_metadata_tag: true

!! name: skos-xref-duplicate
!! description: Using both xref and skos relationship (annotation) to communicate the same mapping
!! seeAlso: https://github.com/geneontology/obographs/issues/102
!! unstable: true
idspace: skos http://www.w3.org/2004/02/skos/core#

[Term]
id: X:1
relationship: skos:exactMatch Y:1
xref: Y:1

[Typedef]
id: skos:exactMatch
is_metadata_tag: true

!! name: alt_id
!! description: Alternative ID for the term

Expand Down
45 changes: 45 additions & 0 deletions tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.json
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{
"graphs" : [ {
"id" : "http://purl.obolibrary.org/obo/skos-xref-duplicate.owl",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
"val" : "1.4"
} ]
},
"nodes" : [ {
"id" : "http://purl.obolibrary.org/obo/X_1",
"type" : "CLASS",
"meta" : {
"xrefs" : [ {
"val" : "Y:1"
} ],
"basicPropertyValues" : [ {
"pred" : "http://www.w3.org/2004/02/skos/core#exactMatch",
"val" : "http://purl.obolibrary.org/obo/Y_1"
} ]
}
}, {
"id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
"lbl" : "database_cross_reference",
"type" : "PROPERTY"
}, {
"id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
"lbl" : "has_obo_format_version",
"type" : "PROPERTY"
}, {
"id" : "http://www.geneontology.org/formats/oboInOwl#id",
"lbl" : "id",
"type" : "PROPERTY"
}, {
"id" : "http://www.w3.org/2004/02/skos/core#exactMatch",
"type" : "PROPERTY",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag",
"val" : "true"
} ]
}
} ]
} ]
}
13 changes: 13 additions & 0 deletions tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.obo
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format-version: 1.2
idspace: skos http://www.w3.org/2004/02/skos/core#
ontology: skos-xref-duplicate

[Term]
id: X:1
xref: Y:1
relationship: skos:exactMatch Y:1

[Typedef]
id: skos:exactMatch
is_metadata_tag: true

53 changes: 53 additions & 0 deletions tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.ofn
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Prefix(:=<http://purl.obolibrary.org/obo/skos-xref-duplicate.owl#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Prefix(skos:=<http://www.w3.org/2004/02/skos/core#>)


Ontology(<http://purl.obolibrary.org/obo/skos-xref-duplicate.owl>
Annotation(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "1.4")

Declaration(Class(<http://purl.obolibrary.org/obo/X_1>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#is_metadata_tag>))
Declaration(AnnotationProperty(skos:exactMatch))
############################
# Annotation Properties
############################

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasDbXref> (database_cross_reference)

AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasDbXref> "database_cross_reference")

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> (has_obo_format_version)

AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "has_obo_format_version")

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#id> (id)

AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#id> "id")

# Annotation Property: skos:exactMatch (skos:exactMatch)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> skos:exactMatch "skos:exactMatch")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#is_metadata_tag> skos:exactMatch "true"^^xsd:boolean)



############################
# Classes
############################

# Class: <http://purl.obolibrary.org/obo/X_1> (<http://purl.obolibrary.org/obo/X_1>)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/X_1> "Y:1")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/X_1> "X:1")
AnnotationAssertion(skos:exactMatch <http://purl.obolibrary.org/obo/X_1> <http://purl.obolibrary.org/obo/Y_1>)


)
90 changes: 90 additions & 0 deletions tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/skos-xref-duplicate.owl#"
xml:base="http://purl.obolibrary.org/obo/skos-xref-duplicate.owl"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/skos-xref-duplicate.owl">
<oboInOwl:hasOBOFormatVersion>1.4</oboInOwl:hasOBOFormatVersion>
</owl:Ontology>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
<rdfs:label>database_cross_reference</rdfs:label>
</owl:AnnotationProperty>



<!-- http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion">
<rdfs:label>has_obo_format_version</rdfs:label>
</owl:AnnotationProperty>



<!-- http://www.geneontology.org/formats/oboInOwl#id -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
<rdfs:label>id</rdfs:label>
</owl:AnnotationProperty>



<!-- http://www.geneontology.org/formats/oboInOwl#is_metadata_tag -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#is_metadata_tag"/>



<!-- http://www.w3.org/2004/02/skos/core#exactMatch -->

<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#exactMatch">
<oboInOwl:id>skos:exactMatch</oboInOwl:id>
<oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag>
</owl:AnnotationProperty>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://purl.obolibrary.org/obo/X_1 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/X_1">
<oboInOwl:hasDbXref>Y:1</oboInOwl:hasDbXref>
<oboInOwl:id>X:1</oboInOwl:id>
<skos:exactMatch rdf:resource="http://purl.obolibrary.org/obo/Y_1"/>
</owl:Class>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->

5 changes: 5 additions & 0 deletions tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.meta.yaml
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name: skos-xref-duplicate
name: skos-xref-duplicate
description: Using both xref and skos relationship (annotation) to communicate the same mapping
seeAlso: https://github.com/geneontology/obographs/issues/102
unstable: true
13 changes: 13 additions & 0 deletions tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.obo
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format-version: 1.4
ontology: skos-xref-duplicate
idspace: skos http://www.w3.org/2004/02/skos/core#

[Term]
id: X:1
relationship: skos:exactMatch Y:1
xref: Y:1

[Typedef]
id: skos:exactMatch
is_metadata_tag: true

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