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Update OWL API to 4.5.26 #1135

Merged
merged 13 commits into from
Sep 20, 2023
Merged

Update OWL API to 4.5.26 #1135

merged 13 commits into from
Sep 20, 2023

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matentzn
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@matentzn matentzn commented Aug 2, 2023

Resolves #1129

  • docs/ have been added/updated (not necessary)
  • tests have been added/updated
  • mvn verify says all tests pass
  • mvn site says all JavaDocs correct
  • CHANGELOG.md has been updated

The last OWL API version (4.5.25) had some major issues with the way complex turtle axioms are written, see #1129. This version solves this problem.

</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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Excellent, thank you for the clarification.

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The following ontologies changed their DL profile status:

clo owl2_dl True False
ecto owl2_dl True False
envo owl2_dl True False
foodon owl2_dl True False
iceo owl2_dl True False
maxo owl2_dl True False
ngbo owl2_dl True False
obi owl2_dl True False
swo owl2_dl True False

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@balhoff suggests could be explained by owlcs/owlapi#1094

@matentzn matentzn added this to the Robot 1.9.5 milestone Aug 24, 2023
@matentzn matentzn mentioned this pull request Aug 24, 2023
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(For the eternal records, the violations are all true positive violations, e.g.)

~/tools/robot validate-profile -I http://purl.obolibrary.org/obo/envo.owl --profile DL
OWL 2 DL Profile Report: Ontology and imports closure NOT in profile. The following violations are present:
Use of unknown datatype: rdfs:anyURI [Declaration(Datatype(rdfs:anyURI)) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo.owl>) VersionIRI(<http://purl.obolibrary.org/obo/envo/releases/2023-02-13/envo.owl>))]

PROFILE VIOLATION ERROR http://purl.obolibrary.org/obo/envo.owl violates profile DL
For details see: http://robot.obolibrary.org/validate-profile#profile-violation-error
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.

@jamesaoverton jamesaoverton merged commit 797cc73 into master Sep 20, 2023
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robot outputs invalid turtle syntax
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