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Feb 9, 2023
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Update to OWLAPI 4.5.24, building on #1005 #1086

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5 changes: 4 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -6,7 +6,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [Unreleased]
- Downgrade SnakeYaml to 1.31 [#1070]
- Upgrade OWLAPI to 4.5.24 [#1086]
- Downgrade SnakeYaml to 1.31 [#1071]

## [1.9.1] - 2022-10-28

Expand Down Expand Up @@ -332,6 +333,8 @@ First official release of ROBOT!
[`template`]: http://robot.obolibrary.org/template
[`validate`]: http://robot.obolibrary.org/validate

[#1086]: https://github.com/ontodev/robot/pull/1086
[#1071]: https://github.com/ontodev/robot/pull/1071
[#1061]: https://github.com/ontodev/robot/issues/1061
[#1030]: https://github.com/ontodev/robot/issues/1030
[#1026]: https://github.com/ontodev/robot/issues/1026
Expand Down
2 changes: 1 addition & 1 deletion docs/examples/example.obo
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@@ -1,7 +1,7 @@
format-version: 1.2
remark: Comment from annotations.ttl file.
ontology: https://github.com/ontodev/robot/examples/edit.owl
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)
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)

[Term]
id: UBERON:0000061
Expand Down
49 changes: 35 additions & 14 deletions docs/examples/example2_defined_by.owl
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Expand Up @@ -31,7 +31,7 @@

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</rdfs:label>
<rdfs:label>definition</rdfs:label>
</owl:AnnotationProperty>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
Expand All @@ -45,19 +45,19 @@
<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/some_other_ont.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">editor note</rdfs:label>
<rdfs:label>editor note</rdfs:label>
</owl:AnnotationProperty>



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

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232">
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">curator notes</rdfs:label>
<rdfs:label>curator notes</rdfs:label>
</owl:AnnotationProperty>


Expand Down Expand Up @@ -121,6 +121,14 @@



<!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral -->

<rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral">
<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
</rdf:Description>



<!-- http://www.w3.org/2001/XMLSchema#string -->

<rdf:Description rdf:about="http://www.w3.org/2001/XMLSchema#string">
Expand All @@ -145,7 +153,7 @@
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</rdfs:label>
<rdfs:label>part_of</rdfs:label>
</owl:ObjectProperty>


Expand All @@ -166,7 +174,7 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000061">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/some_other_ont.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">anatomical structure</rdfs:label>
<rdfs:label>anatomical structure</rdfs:label>
</owl:Class>


Expand All @@ -182,7 +190,7 @@
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">organ</rdfs:label>
<rdfs:label>organ</rdfs:label>
</owl:Class>


Expand Down Expand Up @@ -226,7 +234,7 @@

<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv1">
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/pcl/some_other_ont.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 1</rdfs:label>
<rdfs:label>dummy individal 1</rdfs:label>
</owl:NamedIndividual>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0013702_indv1"/>
Expand All @@ -241,7 +249,7 @@

<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv2">
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/pcl/some_other_ont.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 2</rdfs:label>
<rdfs:label>dummy individal 2</rdfs:label>
</owl:NamedIndividual>


Expand All @@ -250,7 +258,7 @@

<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv3">
<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 3</rdfs:label>
<rdfs:label>dummy individal 3</rdfs:label>
</owl:NamedIndividual>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0013702_indv3"/>
Expand All @@ -265,7 +273,7 @@

<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv4">
<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 4</rdfs:label>
<rdfs:label>dummy individal 4</rdfs:label>
</owl:NamedIndividual>


Expand All @@ -274,10 +282,23 @@

<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv5">
<rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 5</rdfs:label>
<rdfs:label>dummy individal 5</rdfs:label>
</owl:NamedIndividual>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotations
//
///////////////////////////////////////////////////////////////////////////////////////
-->

<rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral"/>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.24) https://github.com/owlcs/owlapi -->

34 changes: 22 additions & 12 deletions docs/examples/metrics_all.json
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Expand Up @@ -30,8 +30,8 @@
"dt_builtin_count_incl": 2,
"dt_notbuiltin_count": 0,
"dt_notbuiltin_count_incl": 0,
"expressivity": "SRIQ",
"expressivity_incl": "SRIQ",
"expressivity": "UCINTERIQ",
"expressivity_incl": "UCINTERIQ",
"gci_count": 0,
"gci_count_incl": 0,
"gci_hidden_count": 105,
Expand All @@ -46,8 +46,8 @@
"most_freq_concept_incl": "http://purl.obolibrary.org/obo/UBERON_0007530",
"multiple_inheritance_count": 103,
"multiple_inheritance_count_incl": 103,
"named_supercl_count_max": 1,
"named_supercl_count_max_incl": 1,
"named_supercl_count_max": 5,
"named_supercl_count_max_incl": 5,
"obj_property_count": 49,
"obj_property_count_incl": 49,
"ontology_anno_count": 0,
Expand Down Expand Up @@ -99,16 +99,20 @@
"InverseObjectProperties"
],
"constructs": [
"ROLE_INVERSE",
"Q",
"R",
"S",
"I"
"CONCEPT_UNION",
"CONCEPT_INTERSECTION",
"FULL_EXISTENTIAL",
"ROLE_COMPLEX"
],
"constructs_incl": [
"ROLE_INVERSE",
"Q",
"R",
"S",
"I"
"CONCEPT_UNION",
"CONCEPT_INTERSECTION",
"FULL_EXISTENTIAL",
"ROLE_COMPLEX"
],
"datatypes_builtin": [
"XSD_STRING",
Expand Down Expand Up @@ -172,12 +176,17 @@
"foaf": "http://xmlns.com/foaf/0.1/",
"BSPO": "http://purl.obolibrary.org/obo/BSPO_"
},
"datatypes_axiom_count": {},
"datatypes_axiom_count_incl": {},
"datatypes_axiom_count": {
"XSD_STRING": 751
},
"datatypes_axiom_count_incl": {
"XSD_STRING": 751
},
"namespace_axiom_count": {
"oboInOwl": 4819,
"IAO": 306,
"UBERON": 1903,
"xsd": 751,
"rdfs": 308,
"BFO": 283,
"obo": 235,
Expand All @@ -189,6 +198,7 @@
"oboInOwl": 4819,
"IAO": 306,
"UBERON": 1903,
"xsd": 751,
"rdfs": 308,
"BFO": 283,
"obo": 235,
Expand Down
4 changes: 2 additions & 2 deletions docs/examples/uvula_inconsistent_explanation.ofn
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Expand Up @@ -19,12 +19,12 @@ Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/CL_0017514>))

# Class: <http://purl.obolibrary.org/obo/UBERON_0003682> (palatal muscle)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0003682> "palatal muscle"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0003682> "palatal muscle")
DisjointClasses(<http://purl.obolibrary.org/obo/UBERON_0003682> <http://purl.obolibrary.org/obo/UBERON_0010235>)

# Class: <http://purl.obolibrary.org/obo/UBERON_0010235> (uvular muscle)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0010235> "uvular muscle"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0010235> "uvular muscle")
SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0010235> <http://purl.obolibrary.org/obo/UBERON_0003682>)


Expand Down
36 changes: 18 additions & 18 deletions docs/examples/uvula_multiple_unsat_2.ofn
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Expand Up @@ -35,19 +35,19 @@ Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/uberon/core#synapsed_

# Object Property: <http://purl.obolibrary.org/obo/BFO_0000050> (part of)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000050> "part of"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000050> "part of")

# Object Property: <http://purl.obolibrary.org/obo/RO_0002202> (develops_from)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002202> "develops_from"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002202> "develops_from")

# Object Property: <http://purl.obolibrary.org/obo/RO_0002219> (surrounded_by)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002219> "surrounded_by"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002219> "surrounded_by")

# Object Property: <http://purl.obolibrary.org/obo/RO_0002473> (composed primarily of)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002473> "composed primarily of"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002473> "composed primarily of")

# Object Property: <http://purl.obolibrary.org/obo/uberon/core#synapsed_by> (synapsed by)

Expand All @@ -65,68 +65,68 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CL_0000100> "moto

# Class: <http://purl.obolibrary.org/obo/UBERON_0000479> (tissue)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0000479> "tissue"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0000479> "tissue")
SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0000479> <http://purl.obolibrary.org/obo/UBERON_0010000>)

# Class: <http://purl.obolibrary.org/obo/UBERON_0001134> (skeletal muscle tissue)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001134> "skeletal muscle tissue"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001134> "skeletal muscle tissue")
SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0001134> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0014892>))

# Class: <http://purl.obolibrary.org/obo/UBERON_0001630> (muscle organ)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001630> "muscle organ"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001630> "muscle organ")

# Class: <http://purl.obolibrary.org/obo/UBERON_0001733> (soft palate)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001733> "soft palate"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0001733> "soft palate")

# Class: <http://purl.obolibrary.org/obo/UBERON_0002384> (connective tissue)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0002384> "connective tissue"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0002384> "connective tissue")
SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0002384> <http://purl.obolibrary.org/obo/UBERON_0000479>)

# Class: <http://purl.obolibrary.org/obo/UBERON_0003082> (myotome)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0003082> "myotome"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0003082> "myotome")

# Class: <http://purl.obolibrary.org/obo/UBERON_0003682> (palatal muscle)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0003682> "palatal muscle"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0003682> "palatal muscle")
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>)))

# Class: <http://purl.obolibrary.org/obo/UBERON_0010000> (multicellular anatomical structure)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0010000> "multicellular anatomical structure"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0010000> "multicellular anatomical structure")

# Class: <http://purl.obolibrary.org/obo/UBERON_0011821> (irregular connective tissue)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011821> "irregular connective tissue"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011821> "irregular connective tissue")
SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0011821> <http://purl.obolibrary.org/obo/UBERON_0002384>)

# Class: <http://purl.obolibrary.org/obo/UBERON_0011822> (dense irregular connective tissue)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011822> "dense irregular connective tissue"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011822> "dense irregular connective tissue")
SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0011822> <http://purl.obolibrary.org/obo/UBERON_0011821>)
SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0011822> <http://purl.obolibrary.org/obo/UBERON_0011823>)

# Class: <http://purl.obolibrary.org/obo/UBERON_0011823> (dense connective tissue)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011823> "dense connective tissue"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0011823> "dense connective tissue")

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

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

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

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0014892> "skeletal muscle organ"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0014892> "skeletal muscle organ")
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>)))

# Class: <http://purl.obolibrary.org/obo/UBERON_0017650> (developing mesenchymal structure)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0017650> "developing mesenchymal structure"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UBERON_0017650> "developing mesenchymal structure")


DisjointClasses(<http://purl.obolibrary.org/obo/UBERON_0010000> <http://purl.obolibrary.org/obo/UBERON_0011823> <http://purl.obolibrary.org/obo/UBERON_0017650>)
Expand Down
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