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Extend RelatedObjectsHelper.getAxiomSubjects() to missing property axiom types #1187

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merged 8 commits into from
May 1, 2024
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Extend RelatedObjectsHelper.getAxiomSubjects() to missing property axiom types #1187

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e9bc206
Add Object property characteristics, inverses, domains, ranges to bas…
matentzn Mar 10, 2024
c2f0dd2
Reflect changes in domain axioms
matentzn Mar 10, 2024
c7da1a9
Fix another test
matentzn Mar 10, 2024
d2ec7a0
Update template-drop-axiom-remove.owl
matentzn Mar 10, 2024
ba3f8ea
Update template-base.owl
matentzn Mar 10, 2024
001f94a
Add subannotation property to getSubject()
matentzn Mar 10, 2024
1cdebfe
Update CHANGELOG.md
matentzn Mar 10, 2024
663a25f
Merge branch 'master' into issue1108-characteristicsmissingfrombase
jamesaoverton May 1, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [`merge`] and 'annotate' operations '--annotate-defined-by' excludes reserved OWL 2 vocabularies [#1171]
- Handle IRIs that are not entities in export [#1168]
- Fix integration tests [#1181]
- Fix issue with correctly determining base entities [#1108]

## [1.9.5] - 2023-09-20

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9 changes: 9 additions & 0 deletions docs/examples/template-base-filter.owl
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Expand Up @@ -58,6 +58,15 @@
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://example.com/B6C3F1"/>
<rdf:Description rdf:about="http://example.com/F344N"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#decimal"/>
</owl:DatatypeProperty>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://example.com/propery-1"/>
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9 changes: 9 additions & 0 deletions docs/examples/template-base.owl
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Expand Up @@ -58,6 +58,15 @@
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://example.com/B6C3F1"/>
<rdf:Description rdf:about="http://example.com/F344N"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#decimal"/>
</owl:DatatypeProperty>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://example.com/propery-1"/>
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11 changes: 10 additions & 1 deletion docs/examples/template-drop-axiom-filter.owl
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Expand Up @@ -52,6 +52,15 @@
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://example.com/B6C3F1"/>
<rdf:Description rdf:about="http://example.com/F344N"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#decimal"/>
</owl:DatatypeProperty>


Expand Down Expand Up @@ -126,5 +135,5 @@



<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->

9 changes: 9 additions & 0 deletions docs/examples/template-drop-axiom-remove.owl
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Expand Up @@ -52,6 +52,15 @@
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://example.com/B6C3F1"/>
<rdf:Description rdf:about="http://example.com/F344N"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#decimal"/>
</owl:DatatypeProperty>


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56 changes: 56 additions & 0 deletions robot-core/src/main/java/org/obolibrary/robot/RelatedObjectsHelper.java
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Expand Up @@ -1417,6 +1417,14 @@ private static Set<IRI> getAxiomSubjects(OWLAxiom axiom) {
} else {
iris.addAll(getIRIsFromEntities(subject.getSignature()));
}
} else if (axiom instanceof OWLSubAnnotationPropertyOfAxiom) {
OWLSubAnnotationPropertyOfAxiom spAxiom = (OWLSubAnnotationPropertyOfAxiom) axiom;
OWLAnnotationProperty subject = spAxiom.getSubProperty();
if (!subject.isAnonymous()) {
return Sets.newHashSet(subject.asOWLAnnotationProperty().getIRI());
} else {
iris.addAll(getIRIsFromEntities(subject.getSignature()));
}
} else if (axiom instanceof OWLEquivalentDataPropertiesAxiom) {
OWLEquivalentDataPropertiesAxiom eqAxiom = (OWLEquivalentDataPropertiesAxiom) axiom;
for (OWLSubDataPropertyOfAxiom spAxiom : eqAxiom.asSubDataPropertyOfAxioms()) {
Expand Down Expand Up @@ -1492,6 +1500,54 @@ private static Set<IRI> getAxiomSubjects(OWLAxiom axiom) {
for (OWLObjectPropertyExpression expr : spcAxiom.getPropertyChain()) {
iris.addAll(getIRIsFromEntities(expr.getSignature()));
}
} else if (axiom instanceof OWLObjectPropertyCharacteristicAxiom) {
OWLObjectPropertyCharacteristicAxiom chAxiom = (OWLObjectPropertyCharacteristicAxiom) axiom;
OWLObjectPropertyExpression subject = chAxiom.getProperty();
if (!subject.isAnonymous()) {
return Sets.newHashSet(subject.asOWLObjectProperty().getIRI());
} else {
iris.addAll(getIRIsFromEntities(subject.getSignature()));
}
} else if (axiom instanceof OWLObjectPropertyDomainAxiom) {
OWLObjectPropertyDomainAxiom domainAxiom = (OWLObjectPropertyDomainAxiom) axiom;
OWLObjectPropertyExpression subject = domainAxiom.getProperty();
if (!subject.isAnonymous()) {
return Sets.newHashSet(subject.asOWLObjectProperty().getIRI());
} else {
iris.addAll(getIRIsFromEntities(subject.getSignature()));
}
} else if (axiom instanceof OWLObjectPropertyRangeAxiom) {
OWLObjectPropertyRangeAxiom rangeAxiom = (OWLObjectPropertyRangeAxiom) axiom;
OWLObjectPropertyExpression subject = rangeAxiom.getProperty();
if (!subject.isAnonymous()) {
return Sets.newHashSet(subject.asOWLObjectProperty().getIRI());
} else {
iris.addAll(getIRIsFromEntities(subject.getSignature()));
}
} else if (axiom instanceof OWLDataPropertyDomainAxiom) {
OWLDataPropertyDomainAxiom domainAxiom = (OWLDataPropertyDomainAxiom) axiom;
OWLDataPropertyExpression subject = domainAxiom.getProperty();
if (!subject.isAnonymous()) {
return Sets.newHashSet(subject.asOWLDataProperty().getIRI());
} else {
iris.addAll(getIRIsFromEntities(subject.getSignature()));
}
} else if (axiom instanceof OWLDataPropertyRangeAxiom) {
OWLDataPropertyRangeAxiom rangeAxiom = (OWLDataPropertyRangeAxiom) axiom;
OWLDataPropertyExpression subject = rangeAxiom.getProperty();
if (!subject.isAnonymous()) {
return Sets.newHashSet(subject.asOWLDataProperty().getIRI());
} else {
iris.addAll(getIRIsFromEntities(subject.getSignature()));
}
} else if (axiom instanceof OWLInverseObjectPropertiesAxiom) {
OWLInverseObjectPropertiesAxiom iopAxiom = (OWLInverseObjectPropertiesAxiom) axiom;
OWLObjectPropertyExpression subject = iopAxiom.getFirstProperty();
if (!subject.isAnonymous()) {
return Sets.newHashSet(subject.asOWLObjectProperty().getIRI());
} else {
iris.addAll(getIRIsFromEntities(subject.getSignature()));
}
} else {
logger.warn("Axiom type not supported: " + axiom.getClass().toString());
}
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