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Make repair command more flexible #1194

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May 13, 2024
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Make repair command more flexible #1194

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57b9f36
Make repair command more flexible
matentzn Apr 8, 2024
8ca3df4
Update CHANGELOG.md
matentzn Apr 8, 2024
5b59fc5
Update repair.md
matentzn May 2, 2024
8af165c
Merge branch 'master' into repair-merge-annotations
jamesaoverton May 13, 2024
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297 changes: 297 additions & 0 deletions docs/examples/uberon_axiom_annotation_merged.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/uberon.owl#"
xml:base="http://purl.obolibrary.org/obo/uberon.owl"
xmlns:obo="http://purl.obolibrary.org/obo/"
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:foaf="http://xmlns.com/foaf/0.1/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon.owl"/>



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




<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000232 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232"/>



<!-- http://purl.obolibrary.org/obo/RO_0002174 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002174"/>



<!-- http://purl.obolibrary.org/obo/RO_0002175 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002175"/>



<!-- http://purl.obolibrary.org/obo/UBPROP_0000001 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000001"/>



<!-- http://purl.obolibrary.org/obo/UBPROP_0000003 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000003"/>



<!-- http://purl.obolibrary.org/obo/UBPROP_0000007 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000007"/>



<!-- http://purl.obolibrary.org/obo/UBPROP_0000008 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000008"/>



<!-- http://purl.obolibrary.org/obo/UBPROP_0000009 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000009"/>



<!-- http://purl.obolibrary.org/obo/UBPROP_0000012 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000012"/>



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

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



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

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



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

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



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

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



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

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



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

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



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

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



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

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



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

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



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

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



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

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



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

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



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

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



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

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



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

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



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

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



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

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



<!-- http://xmlns.com/foaf/0.1/depicted_by -->

<owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/depicted_by"/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://purl.obolibrary.org/obo/BFO_0000050 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<oboInOwl:hasDbXref>BFO:0000050</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>part_of</oboInOwl:id>
<oboInOwl:shorthand>part_of</oboInOwl:shorthand>
<rdfs:label>part_of</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/BFO_0000051 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<oboInOwl:hasDbXref>BFO:0000051</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>has_part</oboInOwl:id>
<oboInOwl:shorthand>has_part</oboInOwl:shorthand>
<rdfs:label>has_part</rdfs:label>
</owl:ObjectProperty>



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




<!-- http://purl.obolibrary.org/obo/UBERON_0000062 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000062">
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Anatomical structure that performs a specific function or group of functions [WP].</obo:IAO_0000115>
<oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page1"/>
<oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page2"/>
<oboInOwl:hasDbXref rdf:resource="http://linkedlifedata.com/resource/umls/id/C0178784"/>
<oboInOwl:hasDbXref rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Organ"/>
<oboInOwl:hasDbXref>WBbt:0003760</oboInOwl:hasDbXref>
<oboInOwl:hasRelatedSynonym>anatomical unit</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>body organ</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>element</oboInOwl:hasRelatedSynonym>
<oboInOwl:id>UBERON:0000062</oboInOwl:id>
<rdfs:label>organ</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Anatomical structure that performs a specific function or group of functions [WP].</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page1"/>
<oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page2"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
<owl:annotatedTarget>body organ</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:resource="UBERON:123"/>
<oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page1"/>
<oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page2"/>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/UBERON_0000467 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000467"/>
</rdf:RDF>



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

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