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Update OWL API to 4.5.26 #1135

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Sep 20, 2023
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Update OWL API to 4.5.26 #1135

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7c6349a
Update OWL API to 4.5.26
matentzn Aug 2, 2023
b953334
Update subset_result.owl
matentzn Aug 2, 2023
99796aa
Update files
matentzn Aug 3, 2023
a234fdd
Update subset_result.owl
matentzn Aug 4, 2023
c946df0
Update merged2.owl
matentzn Aug 4, 2023
a3f3b4e
Update pom.xml
matentzn Aug 4, 2023
51a5afb
Update subset_result.owl
matentzn Aug 4, 2023
8e55f46
Update merged2.owl
matentzn Aug 5, 2023
d537bb8
Merge branch 'rename-edit-annotated' into owlapi4526
matentzn Aug 5, 2023
a968860
Update merged2.owl
matentzn Aug 5, 2023
6a642a7
Merge branch 'master' into owlapi4526
matentzn Aug 5, 2023
8dfc74d
Update CHANGELOG.md
matentzn Aug 5, 2023
1e05594
Merge branch 'master' into owlapi4526
jamesaoverton Sep 20, 2023
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Updated ELK from 0.4.3 to 0.5.0. [#999]. This is an important change as ELK 0.5.0 is more complete than 0.4.3, which means that it will potentially uncover inferences, in particular unsatisfiable classes, which were not recognised by ELK 0.4.3.
- Add support for pluggable commands [#1119]

### Changed
- Migrate to OWL API 4.5.26 to deal with [broken turtle serialiser](https://github.com/ontodev/robot/issues/1129). [#1135]
- Improvements to `export` and `report` for XLSX format [#1148]

## [1.9.4] - 2023-05-23

### Changed
Expand Down Expand Up @@ -369,6 +373,8 @@ First official release of ROBOT!
[`template`]: http://robot.obolibrary.org/template
[`validate`]: http://robot.obolibrary.org/validate

[#1148]: https://github.com/ontodev/robot/pull/1148
[#1135]: https://github.com/ontodev/robot/pull/1135
[#1119]: https://github.com/ontodev/robot/pull/1119
[#1100]: https://github.com/ontodev/robot/pull/1100
[#1091]: https://github.com/ontodev/robot/issues/1091
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25 changes: 14 additions & 11 deletions docs/examples/subset_result.owl
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Expand Up @@ -25,29 +25,31 @@
<!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">database_cross_reference</rdfs:label>
<rdfs:label>database_cross_reference</rdfs:label>
</owl:AnnotationProperty>



<!-- http://www.geneontology.org/formats/oboInOwl#id -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
<rdfs:label>id</rdfs:label>
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The necessity to add this was the only thing that was really important. @balhoff I wonder if you have an hypothesis why suddenly the id was necessary here to be added?

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or in other words, why suddenly the OWLAPI decided that in the presence of the

    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>

Now the <rdfs:label>id</rdfs:label> was serialised out?

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I added it to this enum in my OWLAPI PR: https://github.com/owlcs/owlapi/pull/1099/files#diff-624125d6c0fdd02198cff3e52ece7ed9a49652cc11b4b68bf8a7970a9e35930dR58

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Excellent, thank you for the clarification.

</owl:AnnotationProperty>



<!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_subset</rdfs:label>
<rdfs:label>in_subset</rdfs:label>
</owl:AnnotationProperty>



<!-- http://www.geneontology.org/formats/oboInOwl#shorthand -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">shorthand</rdfs:label>
<rdfs:label>shorthand</rdfs:label>
</owl:AnnotationProperty>


Expand All @@ -66,10 +68,10 @@
<!-- http://purl.obolibrary.org/obo/BFO_0000050 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
<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: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>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<oboInOwl:hasDbXref>BFO:0000050</oboInOwl:hasDbXref>
<oboInOwl:id>part_of</oboInOwl:id>
<oboInOwl:shorthand>part_of</oboInOwl:shorthand>
</owl:ObjectProperty>


Expand All @@ -88,7 +90,7 @@
<!-- http://purl.obolibrary.org/obo/ONT_1 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ONT_1">
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ONT:1</oboInOwl:id>
<oboInOwl:id>ONT:1</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/test#foo"/>
</owl:Class>

Expand All @@ -103,11 +105,12 @@
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ONT_1"/>
</owl:Restriction>
</rdfs:subClassOf>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ONT:5</oboInOwl:id>
<oboInOwl:id>ONT:5</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/test#foo"/>
</owl:Class>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.9) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->

6 changes: 3 additions & 3 deletions pom.xml
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Expand Up @@ -166,7 +166,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-api</artifactId>
<version>4.5.25</version>
<version>4.5.26</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
Expand All @@ -177,7 +177,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-apibinding</artifactId>
<version>4.5.25</version>
<version>4.5.26</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
Expand All @@ -188,7 +188,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-rio</artifactId>
<version>4.5.25</version>
<version>4.5.26</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
Expand Down
6 changes: 3 additions & 3 deletions robot-core/pom.xml
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Expand Up @@ -86,7 +86,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-api</artifactId>
<version>4.5.25</version>
<version>4.5.26</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
Expand All @@ -97,7 +97,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-apibinding</artifactId>
<version>4.5.25</version>
<version>4.5.26</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
Expand All @@ -108,7 +108,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-rio</artifactId>
<version>4.5.25</version>
<version>4.5.26</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
Expand Down
21 changes: 11 additions & 10 deletions robot-core/src/test/resources/subset_result.owl
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Expand Up @@ -25,29 +25,30 @@
<!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">database_cross_reference</rdfs:label>
<rdfs:label>database_cross_reference</rdfs:label>
</owl:AnnotationProperty>



<!-- http://www.geneontology.org/formats/oboInOwl#id -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
<rdfs:label>id</rdfs:label>
</owl:AnnotationProperty>


<!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_subset</rdfs:label>
<rdfs:label>in_subset</rdfs:label>
</owl:AnnotationProperty>



<!-- http://www.geneontology.org/formats/oboInOwl#shorthand -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">shorthand</rdfs:label>
<rdfs:label>shorthand</rdfs:label>
</owl:AnnotationProperty>


Expand All @@ -67,9 +68,9 @@

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
<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: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>
<oboInOwl:hasDbXref>BFO:0000050</oboInOwl:hasDbXref>
<oboInOwl:id>part_of</oboInOwl:id>
<oboInOwl:shorthand>part_of</oboInOwl:shorthand>
</owl:ObjectProperty>


Expand All @@ -88,7 +89,7 @@
<!-- http://purl.obolibrary.org/obo/ONT_1 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ONT_1">
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ONT:1</oboInOwl:id>
<oboInOwl:id>ONT:1</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/test#foo"/>
</owl:Class>

Expand All @@ -103,7 +104,7 @@
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ONT_1"/>
</owl:Restriction>
</rdfs:subClassOf>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ONT:5</oboInOwl:id>
<oboInOwl:id>ONT:5</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/test#foo"/>
</owl:Class>
</rdf:RDF>
Expand Down