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Update OWL API to 4.5.26#1135

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jamesaoverton merged 13 commits intomasterfrom
owlapi4526
Sep 20, 2023
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Update OWL API to 4.5.26#1135
jamesaoverton merged 13 commits intomasterfrom
owlapi4526

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@matentzn matentzn commented Aug 2, 2023 •
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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.

@matentzn matentzn mentioned this pull request Aug 5, 2023
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matentzn commented Aug 5, 2023
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docs/examples/subset_result.owl

<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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@matentzn matentzn Aug 5, 2023

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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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@balhoff balhoff Aug 7, 2023

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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.

@matentzn matentzn requested review from balhoff and hkir-dev August 5, 2023 13:48
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matentzn commented Aug 22, 2023

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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matentzn commented Aug 22, 2023

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

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@matentzn matentzn added this to the Robot 1.9.5 milestone Aug 24, 2023
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matentzn commented Sep 20, 2023

(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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