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Merge pull request #1194 from ontodev/repair-merge-annotations
Make repair command more flexible
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‎CHANGELOG.md

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@@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [`merge`] and 'annotate' operations '--annotate-defined-by' excludes reserved OWL 2 vocabularies [#1171]
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- Handle IRIs that are not entities in export [#1168]
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- Fix integration tests [#1181]
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- `robot repair` is fixed to be more flexible, to enable partial repairs [#1194]
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- Invalid Xrefs test has been fixed to recognise invalid CURIEs correctly [#1127]
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- Fix issue with correctly determining base entities [#1108]
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‎docs/examples/uberon_axiom_annotation_merged.owl

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<?xml version="1.0"?>
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<rdf:RDF xmlns="http://purl.obolibrary.org/obo/uberon.owl#"
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xml:base="http://purl.obolibrary.org/obo/uberon.owl"
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xmlns:obo="http://purl.obolibrary.org/obo/"
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xmlns:owl="http://www.w3.org/2002/07/owl#"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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xmlns:xml="http://www.w3.org/XML/1998/namespace"
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xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
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xmlns:foaf="http://xmlns.com/foaf/0.1/"
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xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
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xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
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<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon.owl"/>
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<!--
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///////////////////////////////////////////////////////////////////////////////////////
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//
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// Annotation properties
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//
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///////////////////////////////////////////////////////////////////////////////////////
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-->
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<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
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<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
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<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
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<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
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<!-- http://purl.obolibrary.org/obo/IAO_0000232 -->
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<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232"/>
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<!-- http://purl.obolibrary.org/obo/RO_0002174 -->
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<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002174"/>
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<!-- http://purl.obolibrary.org/obo/RO_0002175 -->
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<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002175"/>
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<!-- http://purl.obolibrary.org/obo/UBPROP_0000001 -->
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<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000001"/>
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<!-- http://purl.obolibrary.org/obo/UBPROP_0000003 -->
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<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000003"/>
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<!-- http://purl.obolibrary.org/obo/UBPROP_0000007 -->
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<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000007"/>
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<!-- http://purl.obolibrary.org/obo/UBPROP_0000008 -->
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<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000008"/>
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<!-- http://purl.obolibrary.org/obo/UBPROP_0000009 -->
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<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000009"/>
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<!-- http://purl.obolibrary.org/obo/UBPROP_0000012 -->
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<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000012"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#date_retrieved -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#date_retrieved"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#external_class -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#external_class"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#external_ontology -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#external_ontology"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#hasAlternativeId -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasAlternativeId"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#hasOBONamespace -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#hasSynonymType -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasSynonymType"/>
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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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<!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#notes -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#notes"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#ontology -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#ontology"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#shorthand -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#source -->
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<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#source"/>
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<!-- http://xmlns.com/foaf/0.1/depicted_by -->
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<owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/depicted_by"/>
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<!--
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///////////////////////////////////////////////////////////////////////////////////////
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//
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// Object Properties
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//
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///////////////////////////////////////////////////////////////////////////////////////
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-->
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<!-- http://purl.obolibrary.org/obo/BFO_0000050 -->
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<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
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<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
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<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
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<oboInOwl:hasDbXref>BFO:0000050</oboInOwl:hasDbXref>
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<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
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<oboInOwl:id>part_of</oboInOwl:id>
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<oboInOwl:shorthand>part_of</oboInOwl:shorthand>
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<rdfs:label>part_of</rdfs:label>
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</owl:ObjectProperty>
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<!-- http://purl.obolibrary.org/obo/BFO_0000051 -->
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<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
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<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
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<oboInOwl:hasDbXref>BFO:0000051</oboInOwl:hasDbXref>
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<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
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<oboInOwl:id>has_part</oboInOwl:id>
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<oboInOwl:shorthand>has_part</oboInOwl:shorthand>
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<rdfs:label>has_part</rdfs:label>
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</owl:ObjectProperty>
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<!--
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///////////////////////////////////////////////////////////////////////////////////////
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//
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// Classes
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//
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///////////////////////////////////////////////////////////////////////////////////////
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-->
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<!-- http://purl.obolibrary.org/obo/UBERON_0000062 -->
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<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000062">
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<obo:IAO_0000115>Anatomical structure that performs a specific function or group of functions [WP].</obo:IAO_0000115>
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<oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page1"/>
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<oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page2"/>
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<oboInOwl:hasDbXref rdf:resource="http://linkedlifedata.com/resource/umls/id/C0178784"/>
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<oboInOwl:hasDbXref rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Organ"/>
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<oboInOwl:hasDbXref>WBbt:0003760</oboInOwl:hasDbXref>
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<oboInOwl:hasRelatedSynonym>anatomical unit</oboInOwl:hasRelatedSynonym>
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<oboInOwl:hasRelatedSynonym>body organ</oboInOwl:hasRelatedSynonym>
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<oboInOwl:hasRelatedSynonym>element</oboInOwl:hasRelatedSynonym>
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<oboInOwl:id>UBERON:0000062</oboInOwl:id>
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<rdfs:label>organ</rdfs:label>
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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/UBERON_0000062"/>
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<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
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<owl:annotatedTarget>Anatomical structure that performs a specific function or group of functions [WP].</owl:annotatedTarget>
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<oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page1"/>
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<oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page2"/>
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</owl:Axiom>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
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<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
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<owl:annotatedTarget>body organ</owl:annotatedTarget>
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<oboInOwl:hasDbXref rdf:resource="UBERON:123"/>
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<oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page1"/>
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<oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page2"/>
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</owl:Axiom>
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<!-- http://purl.obolibrary.org/obo/UBERON_0000467 -->
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<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000467"/>
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</rdf:RDF>
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<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
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