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Merge pull request #1086 from ontodev/owlapi-4.5.24
Update to OWLAPI 4.5.24, building on #1005
2 parents 4ac29c4 + 4efec37 commit 60d46f6

19 files changed

+175
-117
lines changed

CHANGELOG.md

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@@ -6,7 +6,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [Unreleased]
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- Downgrade SnakeYaml to 1.31 [#1070]
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- Upgrade OWLAPI to 4.5.24 [#1086]
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- Downgrade SnakeYaml to 1.31 [#1071]
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## [1.9.1] - 2022-10-28
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@@ -332,6 +333,8 @@ First official release of ROBOT!
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[`template`]: http://robot.obolibrary.org/template
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[`validate`]: http://robot.obolibrary.org/validate
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[#1086]: https://github.com/ontodev/robot/pull/1086
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[#1071]: https://github.com/ontodev/robot/pull/1071
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[#1061]: https://github.com/ontodev/robot/issues/1061
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[#1030]: https://github.com/ontodev/robot/issues/1030
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[#1026]: https://github.com/ontodev/robot/issues/1026

docs/examples/example.obo

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@@ -1,7 +1,7 @@
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format-version: 1.2
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remark: Comment from annotations.ttl file.
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ontology: https://github.com/ontodev/robot/examples/edit.owl
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owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001062>))\n############################\n# Classes\n############################\n\n# Class: <http://purl.obolibrary.org/obo/UBERON_0001062> (anatomical entity)\n\nSubClassOf(<http://purl.obolibrary.org/obo/UBERON_0001062> owl:Thing)\n\n\n)
4+
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001062>))\n############################\n# Classes\n############################\n\n# Class: <http://purl.obolibrary.org/obo/UBERON_0001062> (<http://purl.obolibrary.org/obo/UBERON_0001062>)\n\nSubClassOf(<http://purl.obolibrary.org/obo/UBERON_0001062> owl:Thing)\n\n\n)
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[Term]
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id: UBERON:0000061

docs/examples/example2_defined_by.owl

Lines changed: 35 additions & 14 deletions
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@@ -31,7 +31,7 @@
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<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
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<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</rdfs:label>
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<rdfs:label>definition</rdfs:label>
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</owl:AnnotationProperty>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
@@ -45,19 +45,19 @@
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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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<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
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<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
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<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/some_other_ont.owl"/>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">editor note</rdfs:label>
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<rdfs:label>editor note</rdfs:label>
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</owl:AnnotationProperty>
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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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<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
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<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
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<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">curator notes</rdfs:label>
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<rdfs:label>curator notes</rdfs:label>
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</owl:AnnotationProperty>
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@@ -121,6 +121,14 @@
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<!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral -->
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<rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral">
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<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
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</rdf:Description>
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<!-- http://www.w3.org/2001/XMLSchema#string -->
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<rdf:Description rdf:about="http://www.w3.org/2001/XMLSchema#string">
@@ -145,7 +153,7 @@
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<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
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<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
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<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</rdfs:label>
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<rdfs:label>part_of</rdfs:label>
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</owl:ObjectProperty>
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@@ -166,7 +174,7 @@
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<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000061">
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
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<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/some_other_ont.owl"/>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">anatomical structure</rdfs:label>
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<rdfs:label>anatomical structure</rdfs:label>
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</owl:Class>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">organ</rdfs:label>
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<rdfs:label>organ</rdfs:label>
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</owl:Class>
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<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv1">
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<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/pcl/some_other_ont.owl"/>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 1</rdfs:label>
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<rdfs:label>dummy individal 1</rdfs:label>
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</owl:NamedIndividual>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0013702_indv1"/>
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<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv2">
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<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/pcl/some_other_ont.owl"/>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 2</rdfs:label>
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<rdfs:label>dummy individal 2</rdfs:label>
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</owl:NamedIndividual>
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<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv3">
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<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 3</rdfs:label>
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<rdfs:label>dummy individal 3</rdfs:label>
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</owl:NamedIndividual>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0013702_indv3"/>
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<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv4">
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<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 4</rdfs:label>
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<rdfs:label>dummy individal 4</rdfs:label>
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</owl:NamedIndividual>
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<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv5">
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<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 5</rdfs:label>
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<rdfs:label>dummy individal 5</rdfs:label>
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</owl:NamedIndividual>
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<!--
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///////////////////////////////////////////////////////////////////////////////////////
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//
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// Annotations
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//
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///////////////////////////////////////////////////////////////////////////////////////
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-->
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<rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral"/>
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</rdf:RDF>
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<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
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<!-- Generated by the OWL API (version 4.5.24) https://github.com/owlcs/owlapi -->
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docs/examples/metrics_all.json

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"dt_builtin_count_incl": 2,
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"dt_notbuiltin_count": 0,
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"dt_notbuiltin_count_incl": 0,
33-
"expressivity": "SRIQ",
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"expressivity_incl": "SRIQ",
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"expressivity": "UCINTERIQ",
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"expressivity_incl": "UCINTERIQ",
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"gci_count": 0,
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"gci_count_incl": 0,
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"gci_hidden_count": 105,
@@ -46,8 +46,8 @@
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"most_freq_concept_incl": "http://purl.obolibrary.org/obo/UBERON_0007530",
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"multiple_inheritance_count": 103,
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"multiple_inheritance_count_incl": 103,
49-
"named_supercl_count_max": 1,
50-
"named_supercl_count_max_incl": 1,
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"named_supercl_count_max": 5,
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"named_supercl_count_max_incl": 5,
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"obj_property_count": 49,
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"obj_property_count_incl": 49,
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"ontology_anno_count": 0,
@@ -99,16 +99,20 @@
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"InverseObjectProperties"
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],
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"constructs": [
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"ROLE_INVERSE",
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"Q",
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"R",
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"S",
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"I"
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"CONCEPT_UNION",
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"CONCEPT_INTERSECTION",
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"FULL_EXISTENTIAL",
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"ROLE_COMPLEX"
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],
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"constructs_incl": [
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"ROLE_INVERSE",
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"Q",
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"R",
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"S",
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"I"
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"CONCEPT_UNION",
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"CONCEPT_INTERSECTION",
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"FULL_EXISTENTIAL",
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"ROLE_COMPLEX"
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],
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"datatypes_builtin": [
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"XSD_STRING",
@@ -172,12 +176,17 @@
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"foaf": "http://xmlns.com/foaf/0.1/",
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"BSPO": "http://purl.obolibrary.org/obo/BSPO_"
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},
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"datatypes_axiom_count": {},
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"datatypes_axiom_count_incl": {},
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"datatypes_axiom_count": {
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"XSD_STRING": 751
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},
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"datatypes_axiom_count_incl": {
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"XSD_STRING": 751
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},
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"namespace_axiom_count": {
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"oboInOwl": 4819,
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"IAO": 306,
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"UBERON": 1903,
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"xsd": 751,
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"rdfs": 308,
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"BFO": 283,
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"obo": 235,
@@ -189,6 +198,7 @@
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"oboInOwl": 4819,
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"IAO": 306,
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"UBERON": 1903,
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"xsd": 751,
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"rdfs": 308,
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"BFO": 283,
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"obo": 235,

docs/examples/uvula_inconsistent_explanation.ofn

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@@ -19,12 +19,12 @@ Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/CL_0017514>))
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# Class: <http://purl.obolibrary.org/obo/UBERON_0003682> (palatal muscle)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0003682> "palatal muscle"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0003682> "palatal muscle")
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DisjointClasses(<http://purl.obolibrary.org/obo/UBERON_0003682> <http://purl.obolibrary.org/obo/UBERON_0010235>)
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# Class: <http://purl.obolibrary.org/obo/UBERON_0010235> (uvular muscle)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0010235> "uvular muscle"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0010235> "uvular muscle")
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SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0010235> <http://purl.obolibrary.org/obo/UBERON_0003682>)
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docs/examples/uvula_multiple_unsat_2.ofn

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@@ -35,19 +35,19 @@ Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/uberon/core#synapsed_
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# Object Property: <http://purl.obolibrary.org/obo/BFO_0000050> (part of)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000050> "part of"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000050> "part of")
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# Object Property: <http://purl.obolibrary.org/obo/RO_0002202> (develops_from)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002202> "develops_from"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002202> "develops_from")
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# Object Property: <http://purl.obolibrary.org/obo/RO_0002219> (surrounded_by)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002219> "surrounded_by"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002219> "surrounded_by")
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# Object Property: <http://purl.obolibrary.org/obo/RO_0002473> (composed primarily of)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002473> "composed primarily of"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002473> "composed primarily of")
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# Object Property: <http://purl.obolibrary.org/obo/uberon/core#synapsed_by> (synapsed by)
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@@ -65,68 +65,68 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CL_0000100> "moto
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# Class: <http://purl.obolibrary.org/obo/UBERON_0000479> (tissue)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0000479> "tissue"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0000479> "tissue")
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SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0000479> <http://purl.obolibrary.org/obo/UBERON_0010000>)
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# Class: <http://purl.obolibrary.org/obo/UBERON_0001134> (skeletal muscle tissue)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001134> "skeletal muscle tissue"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001134> "skeletal muscle tissue")
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SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0001134> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0014892>))
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# Class: <http://purl.obolibrary.org/obo/UBERON_0001630> (muscle organ)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001630> "muscle organ"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001630> "muscle organ")
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# Class: <http://purl.obolibrary.org/obo/UBERON_0001733> (soft palate)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001733> "soft palate"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001733> "soft palate")
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# Class: <http://purl.obolibrary.org/obo/UBERON_0002384> (connective tissue)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0002384> "connective tissue"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0002384> "connective tissue")
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SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0002384> <http://purl.obolibrary.org/obo/UBERON_0000479>)
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# Class: <http://purl.obolibrary.org/obo/UBERON_0003082> (myotome)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0003082> "myotome"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0003082> "myotome")
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# Class: <http://purl.obolibrary.org/obo/UBERON_0003682> (palatal muscle)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0003682> "palatal muscle"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0003682> "palatal muscle")
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EquivalentClasses(<http://purl.obolibrary.org/obo/UBERON_0003682> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0014892> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001733>)))
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# Class: <http://purl.obolibrary.org/obo/UBERON_0010000> (multicellular anatomical structure)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0010000> "multicellular anatomical structure"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0010000> "multicellular anatomical structure")
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# Class: <http://purl.obolibrary.org/obo/UBERON_0011821> (irregular connective tissue)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011821> "irregular connective tissue"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011821> "irregular connective tissue")
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SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0011821> <http://purl.obolibrary.org/obo/UBERON_0002384>)
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# Class: <http://purl.obolibrary.org/obo/UBERON_0011822> (dense irregular connective tissue)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011822> "dense irregular connective tissue"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011822> "dense irregular connective tissue")
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SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0011822> <http://purl.obolibrary.org/obo/UBERON_0011821>)
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SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0011822> <http://purl.obolibrary.org/obo/UBERON_0011823>)
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# Class: <http://purl.obolibrary.org/obo/UBERON_0011823> (dense connective tissue)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011823> "dense connective tissue"^^xsd:string)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011823> "dense connective tissue")
116116

117117
# Class: <http://purl.obolibrary.org/obo/UBERON_0011899> (epimysium)
118118

119-
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011899> "epimysium"^^xsd:string)
119+
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011899> "epimysium")
120120
SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0011899> <http://purl.obolibrary.org/obo/UBERON_0011822>)
121121

122122
# Class: <http://purl.obolibrary.org/obo/UBERON_0014892> (skeletal muscle organ)
123123

124-
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0014892> "skeletal muscle organ"^^xsd:string)
124+
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0014892> "skeletal muscle organ")
125125
EquivalentClasses(<http://purl.obolibrary.org/obo/UBERON_0014892> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_0001630> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002202> <http://purl.obolibrary.org/obo/UBERON_0003082>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002219> <http://purl.obolibrary.org/obo/UBERON_0011899>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002473> <http://purl.obolibrary.org/obo/UBERON_0001134>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/uberon/core#synapsed_by> <http://purl.obolibrary.org/obo/CL_0000100>)))
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# Class: <http://purl.obolibrary.org/obo/UBERON_0017650> (developing mesenchymal structure)
128128

129-
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0017650> "developing mesenchymal structure"^^xsd:string)
129+
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0017650> "developing mesenchymal structure")
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DisjointClasses(<http://purl.obolibrary.org/obo/UBERON_0010000> <http://purl.obolibrary.org/obo/UBERON_0011823> <http://purl.obolibrary.org/obo/UBERON_0017650>)

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