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Update obo compliance suite using latest robot (#747)
Using robot prerelease from owlcs/owlapi#1102
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250 files changed

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‎tests/input/obo-compliance/alt_id/alt_id.expected.json

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"id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
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"lbl" : "has_obo_format_version",
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"type" : "PROPERTY"
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}, {
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"id" : "http://www.geneontology.org/formats/oboInOwl#id",
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"lbl" : "id",
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"type" : "PROPERTY"
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} ]
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} ]
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}

‎tests/input/obo-compliance/alt_id/alt_id.expected.ofn

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

‎tests/input/obo-compliance/alt_id/alt_id.expected.owl

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<!-- http://www.geneontology.org/formats/oboInOwl#id -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
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<rdfs:label>id</rdfs:label>
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</owl:AnnotationProperty>
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<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
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<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
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‎tests/input/obo-compliance/broad_synonym/broad_synonym.expected.json

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"id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
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"lbl" : "has_obo_format_version",
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"type" : "PROPERTY"
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}, {
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"id" : "http://www.geneontology.org/formats/oboInOwl#id",
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"lbl" : "id",
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"type" : "PROPERTY"
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} ]
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} ]
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}

‎tests/input/obo-compliance/broad_synonym/broad_synonym.expected.ofn

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

‎tests/input/obo-compliance/broad_synonym/broad_synonym.expected.owl

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<!-- http://www.geneontology.org/formats/oboInOwl#id -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
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<rdfs:label>id</rdfs:label>
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</owl:AnnotationProperty>
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<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
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<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
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‎tests/input/obo-compliance/comment/comment.expected.json

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"id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
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"lbl" : "has_obo_format_version",
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"type" : "PROPERTY"
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}, {
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"id" : "http://www.geneontology.org/formats/oboInOwl#id",
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"lbl" : "id",
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"type" : "PROPERTY"
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} ]
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} ]
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}

‎tests/input/obo-compliance/comment/comment.expected.ofn

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

‎tests/input/obo-compliance/comment/comment.expected.owl

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<!-- http://www.geneontology.org/formats/oboInOwl#id -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
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<rdfs:label>id</rdfs:label>
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</owl:AnnotationProperty>
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<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
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<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
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‎tests/input/obo-compliance/consider-annotated/consider-annotated.expected.json

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"meta" : {
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"basicPropertyValues" : [ {
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"pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
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"val" : "X:3"
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"val" : "http://purl.obolibrary.org/obo/X_3"
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} ],
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"deprecated" : true
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}
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"id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
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"lbl" : "has_obo_format_version",
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"type" : "PROPERTY"
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}, {
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"id" : "http://www.geneontology.org/formats/oboInOwl#id",
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"lbl" : "id",
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"type" : "PROPERTY"
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} ]
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} ]
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}

‎tests/input/obo-compliance/consider-annotated/consider-annotated.expected.ofn

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@@ -27,6 +27,10 @@ AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#con
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AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "has_obo_format_version")
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# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#id> (id)
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AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#id> "id")
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############################
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# Class: <http://purl.obolibrary.org/obo/X_1> (<http://purl.obolibrary.org/obo/X_1>)
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AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "PMID:123470") <http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/X_1> "X:3")
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AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "PMID:123470") <http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/X_1> <http://purl.obolibrary.org/obo/X_3>)
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/X_1> "X:1")
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AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/X_1> "true"^^xsd:boolean)
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‎tests/input/obo-compliance/consider-annotated/consider-annotated.expected.owl

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<!-- http://www.geneontology.org/formats/oboInOwl#id -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
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<rdfs:label>id</rdfs:label>
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</owl:AnnotationProperty>
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<!-- http://purl.obolibrary.org/obo/X_1 -->
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<owl:Class rdf:about="http://purl.obolibrary.org/obo/X_1">
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<oboInOwl:consider>X:3</oboInOwl:consider>
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<oboInOwl:consider rdf:resource="http://purl.obolibrary.org/obo/X_3"/>
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<oboInOwl:id>X:1</oboInOwl:id>
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<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
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</owl:Class>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/X_1"/>
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<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#consider"/>
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<owl:annotatedTarget>X:3</owl:annotatedTarget>
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<owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/X_3"/>
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<oboInOwl:source>PMID:123470</oboInOwl:source>
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</owl:Axiom>
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</rdf:RDF>
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<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
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<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
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‎tests/input/obo-compliance/consider/consider.expected.json

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"meta" : {
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"basicPropertyValues" : [ {
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"pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
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"val" : "X:3"
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"val" : "http://purl.obolibrary.org/obo/X_3"
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} ],
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"deprecated" : true
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}
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"id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
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"lbl" : "has_obo_format_version",
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"type" : "PROPERTY"
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}, {
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"id" : "http://www.geneontology.org/formats/oboInOwl#id",
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"lbl" : "id",
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"type" : "PROPERTY"
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} ]
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} ]
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}

‎tests/input/obo-compliance/consider/consider.expected.ofn

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AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "has_obo_format_version")
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# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#id> (id)
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AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#id> "id")
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############################
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# Class: <http://purl.obolibrary.org/obo/X_1> (<http://purl.obolibrary.org/obo/X_1>)
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/X_1> "X:3")
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/X_1> <http://purl.obolibrary.org/obo/X_3>)
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/X_1> "X:1")
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AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/X_1> "true"^^xsd:boolean)
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‎tests/input/obo-compliance/consider/consider.expected.owl

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<!-- http://www.geneontology.org/formats/oboInOwl#id -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
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<rdfs:label>id</rdfs:label>
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</owl:AnnotationProperty>
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<!-- http://purl.obolibrary.org/obo/X_1 -->
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<owl:Class rdf:about="http://purl.obolibrary.org/obo/X_1">
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<oboInOwl:consider>X:3</oboInOwl:consider>
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<oboInOwl:consider rdf:resource="http://purl.obolibrary.org/obo/X_3"/>
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<oboInOwl:id>X:1</oboInOwl:id>
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<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
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</owl:Class>
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</rdf:RDF>
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<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
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<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
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‎tests/input/obo-compliance/created_by-annotated/created_by-annotated.expected.json

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"val" : "ORCID:1234"
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} ]
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}
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}, {
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"id" : "http://www.geneontology.org/formats/oboInOwl#created_by",
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"lbl" : "created by",
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"type" : "PROPERTY"
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}, {
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"id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
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"lbl" : "has_obo_format_version",
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"type" : "PROPERTY"
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}, {
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"id" : "http://www.geneontology.org/formats/oboInOwl#id",
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"lbl" : "id",
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"type" : "PROPERTY"
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} ]
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} ]
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}

‎tests/input/obo-compliance/created_by-annotated/created_by-annotated.expected.ofn

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# Annotation Properties
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# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#created_by> (created by)
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AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#created_by> "created by")
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# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> (has_obo_format_version)
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AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "has_obo_format_version")
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# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#id> (id)
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AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#id> "id")
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############################

‎tests/input/obo-compliance/created_by-annotated/created_by-annotated.expected.owl

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<!-- http://www.geneontology.org/formats/oboInOwl#created_by -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by"/>
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by">
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<rdfs:label>created by</rdfs:label>
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</owl:AnnotationProperty>
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<!-- http://www.geneontology.org/formats/oboInOwl#id -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
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<rdfs:label>id</rdfs:label>
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</owl:AnnotationProperty>
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<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
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<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
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‎tests/input/obo-compliance/created_by/created_by.expected.json

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"val" : "username"
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} ]
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}
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}, {
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"id" : "http://www.geneontology.org/formats/oboInOwl#created_by",
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"lbl" : "created by",
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"type" : "PROPERTY"
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}, {
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"id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
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"lbl" : "has_obo_format_version",
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"type" : "PROPERTY"
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}, {
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"id" : "http://www.geneontology.org/formats/oboInOwl#id",
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"lbl" : "id",
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"type" : "PROPERTY"
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} ]
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} ]
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}

‎tests/input/obo-compliance/created_by/created_by.expected.ofn

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# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#created_by> (created by)
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AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#created_by> "created by")
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# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> (has_obo_format_version)
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AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "has_obo_format_version")
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# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#id> (id)
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AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#id> "id")
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############################

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