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 $@.owl
In order to remove all axioms of this kind:
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBcv_0000002"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Phenotype that is a defect in thermotaxis (GO:0043052). 'thermotaxis' is defined as: '$sub_GO:0043052'</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)
Commits related to this issue
- Merge pull request #585 from beckyjackson/532-fix Removing definitions for #532 — committed to ontodev/robot by jamesaoverton 5 years ago
I think having an
--ignore-axiom-annotations <true/false>option would be great.