robot: Removing definitions seems to not work

I am trying to run:

robot remove --input o.owl --term-file simple-rm.txt --axioms annotation --trim false -o $@.owl

In order to remove all axioms of this kind:

<owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBcv_0000002"/>
        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phenotype that is a defect in thermotaxis (GO:0043052). &apos;thermotaxis&apos; is defined as: &apos;$sub_GO:0043052&apos;</owl:annotatedTarget>
        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBC:DOS</oboInOwl:hasDbXref>
</owl:Axiom>

I tried to add hasDBXref iri to the term file as well, and tried signature true. The goal is to remove all definitions of the classes in the term file, with or without axiom annotations on them… What is the best way to accomplish this?

git clone https://github.com/monarch-ebi-dev/robot_test.git
cd robot_test
make fail_remove_definitions
diff o.owl fail_remove_definitions.owl

Thaaaanks! 😃

About this issue

  • Original URL
  • State: closed
  • Created 5 years ago
  • Comments: 16 (16 by maintainers)

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Most upvoted comments

I think having an --ignore-axiom-annotations <true/false> option would be great.