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Fix repair merge axiom annotations #1223

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Nov 12, 2024
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Fix repair merge axiom annotations #1223

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0acc87e
Normalise docs/examples/uberon_axiom_annotation_merging.owl
matentzn Nov 11, 2024
c4e9708
Remove restriction on ROBOT repair to work only on annotation axioms
matentzn Nov 11, 2024
1d3a6ba
Add repair axiom annotation merge bug to Changelog
matentzn Nov 11, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Fixed
- Output inferred object property assertions using Whelk reasoner, by updating to Whelk 1.1.3. [#1121]
- Bug was fixed that caused logical axioms with axiom annotations not to be processed correctly when merging axiom annotations [#1223]

### Changed
- Update Whelk to 1.2.1 [#1221]
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16 changes: 15 additions & 1 deletion docs/examples/uberon_axiom_annotation_merged.owl
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Expand Up @@ -247,9 +247,16 @@



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

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



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

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000062">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ROBOT_SuperClass"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
Expand All @@ -268,6 +275,13 @@
<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://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/ROBOT_SuperClass"/>
<rdfs:comment>Comment A</rdfs:comment>
<rdfs:comment>Comment B</rdfs:comment>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
Expand All @@ -293,5 +307,5 @@



<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->

95 changes: 59 additions & 36 deletions docs/examples/uberon_axiom_annotation_merging.owl
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@@ -1,14 +1,14 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/uberon.owl#"
xml:base="http://purl.obolibrary.org/obo/uberon.owl"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
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:obo="http://purl.obolibrary.org/obo/"
xmlns:foaf="http://xmlns.com/foaf/0.1/">
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon.owl"/>


Expand Down Expand Up @@ -214,11 +214,11 @@
<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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BFO:0000050</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</oboInOwl:id>
<oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</oboInOwl:shorthand>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</rdfs:label>
<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>


Expand All @@ -227,11 +227,11 @@

<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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BFO:0000051</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_part</oboInOwl:id>
<oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_part</oboInOwl:shorthand>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_part</rdfs:label>
<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>


Expand All @@ -247,62 +247,85 @@



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

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



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

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000062">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ROBOT_SuperClass"/>
<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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anatomical structure that performs a specific function or group of functions [WP].</obo:IAO_0000115>
<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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">WBbt:0003760</oboInOwl:hasDbXref>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">anatomical unit</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">body organ</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">element</oboInOwl:hasRelatedSynonym>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UBERON:0000062</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">organ</rdfs:label>
<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://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">body organ</owl:annotatedTarget>
<oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page1"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/ROBOT_SuperClass"/>
<rdfs:comment>Comment A</rdfs:comment>
</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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">body organ</owl:annotatedTarget>
<oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page2"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/ROBOT_SuperClass"/>
<rdfs:comment>Comment B</rdfs:comment>
</owl:Axiom>
<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"/>
</owl:Axiom>
<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/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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">body organ</owl:annotatedTarget>
<owl:annotatedTarget>body organ</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:resource="UBERON:123"/>
</owl:Axiom>
<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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anatomical structure that performs a specific function or group of functions [WP].</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page1"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
<owl:annotatedTarget>body organ</owl:annotatedTarget>
<oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page1"/>
</owl:Axiom>
<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 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anatomical structure that performs a specific function or group of functions [WP].</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page2"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
<owl:annotatedTarget>body organ</owl:annotatedTarget>
<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 0.0.1-SNAPSHOT) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi -->

6 changes: 2 additions & 4 deletions robot-core/src/main/java/org/obolibrary/robot/RepairOperation.java
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Expand Up @@ -152,10 +152,8 @@ public static void mergeAxiomAnnotations(OWLOntology ontology) {
Set<OWLAxiom> newAxioms = new HashSet<>();
for (Map.Entry<OWLAxiom, Set<OWLAnnotation>> mergedAxiom : mergedAxioms.entrySet()) {
OWLAxiom axiom = mergedAxiom.getKey();
if (axiom.isAnnotationAxiom()) {
OWLAxiom newAxiom = axiom.getAnnotatedAxiom(mergedAxiom.getValue());
newAxioms.add(newAxiom);
}
OWLAxiom newAxiom = axiom.getAnnotatedAxiom(mergedAxiom.getValue());
newAxioms.add(newAxiom);
}
manager.addAxioms(ontology, newAxioms);
}
Expand Down
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