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Relax command extension #1188

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merged 4 commits into from
May 2, 2024
Merged

Relax command extension #1188

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d7942b8
First draft of relax command extension
matentzn Mar 10, 2024
f7afce1
Update docs/relax.md
matentzn Mar 12, 2024
421c96f
Merge branch 'master' into issue1060-relaxfixes
matentzn May 2, 2024
84fcfbc
Remove short options for enfore-obo-format and exclude named classes
matentzn May 2, 2024
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## [Unreleased]

## Changed
- Add `--enforce-obo-format`, `--exclude-named-classes` and `--include-subclass-of` features to relax command [#1060, #1183]

### Fixed
- '--annotate-with-source true' does not work with extract --method subset [#1160]
- Fix how Template adds entities to the QuotedEntityChecker [#1104]
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233 changes: 233 additions & 0 deletions docs/examples/relaxed-enforced-obo.owl
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@@ -0,0 +1,233 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/robot/tests/relaxed2.owl#"
xml:base="http://purl.obolibrary.org/obo/robot/tests/relaxed2.owl"
xmlns:owl="http://www.w3.org/2002/07/owl#"
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:rdfs="http://www.w3.org/2000/01/rdf-schema#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/robot/tests/relaxed2.owl"/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




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

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/ROBOT_R">
<rdfs:label xml:lang="en">R</rdfs:label>
</owl:ObjectProperty>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->




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

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_A">
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/ROBOT_A1"/>
<rdfs:label xml:lang="en">A (Named Equivalent)</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ROBOT_A1 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_A1">
<rdfs:label xml:lang="en">A1</rdfs:label>
</owl:Class>



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

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_B">
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/ROBOT_B1"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ROBOT_R"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ROBOT_B2"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:label xml:lang="en">B (SubClass example)</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ROBOT_B1 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_B1">
<rdfs:label xml:lang="en">B1</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ROBOT_B2 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_B2">
<rdfs:label xml:lang="en">B2</rdfs:label>
</owl:Class>



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

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_C">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ROBOT_R"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ROBOT_C1"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ROBOT_R"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ROBOT_C1"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label xml:lang="en">C (Equivalent Simple Existential)</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ROBOT_C1 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_C1">
<rdfs:label xml:lang="en">C1 (Equivalent Simple Existential)</rdfs:label>
</owl:Class>



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

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_E">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/ROBOT_E1"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ROBOT_R"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ROBOT_E2"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ROBOT_R"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ROBOT_E3"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ROBOT_R"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ROBOT_R"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ROBOT_E5"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ROBOT_R"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ROBOT_E4"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ROBOT_R"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minQualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/ROBOT_E6"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ROBOT_E1"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ROBOT_R"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ROBOT_E2"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ROBOT_R"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ROBOT_E3"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ROBOT_R"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ROBOT_E6"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label xml:lang="en">E (Complex existential)</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ROBOT_E1 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_E1">
<rdfs:label xml:lang="en">E1</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ROBOT_E2 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_E2">
<rdfs:label xml:lang="en">E2</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ROBOT_E3 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_E3">
<rdfs:label xml:lang="en">E3</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ROBOT_E4 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_E4">
<rdfs:label xml:lang="en">E4</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ROBOT_E5 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_E5">
<rdfs:label xml:lang="en">E5</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ROBOT_E6 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ROBOT_E6">
<rdfs:label xml:lang="en">E6</rdfs:label>
</owl:Class>
</rdf:RDF>



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

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