Open stuppie opened 6 years ago
$ owltools MYFILE.owl -o -h
-o [-f FORMAT] [--prefix PREFIX URI]* FILE writes source ontology.
e.g.
owltools MYFILE.owl -o -f ofn --prefix FOO http://example.org/foo MYFILE-out.ofn
should work with any owlapi prefix-enabled format
(note prefix definitions are a purely syntactic feature and semantically invisible to the owlapi)
Also for many basic ontology release operations the recommendation is to use robot.
Thanks for the quick response!!
It still didn't work however. Example:
owltools doid-edit.owl --merge tmp.ttl -o -f ofn --prefix skos "http://www.w3.org/2004/02/skos/core#" doid-edit.owl
where doid-edit.owl
is: https://github.com/DiseaseOntology/HumanDiseaseOntology/blob/master/src/ontology/doid-edit.owl
and tmp.ttl contains:
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
obo:DOID_7880 skos:broadMatch "XXX"^^xsd:string .
I get the following lines in the output file:
Declaration(AnnotationProperty(<http://www.w3.org/2004/02/skos/core#broadMatch>))
AnnotationAssertion(<http://www.w3.org/2004/02/skos/core#broadMatch> obo:DOID_7880 "XXX"^^xsd:string)
where I'm expecting
Prefix(skos:=<http://www.w3.org/2004/02/skos/core#>)
Declaration(AnnotationProperty(skos:broadMatch))
AnnotationAssertion(skos:broadMatch obo:DOID_7880 "XXX"^^xsd:string)
I know they're equivalent, but.. just for git reasons, I'd like it to be the curie
Is there a way (preferably on the command line) to add a prefix definition to an ontology?
To give my specific usage, I am trying to merge some triples into an existing ontology however if there is a prefix defined in the triples that doesn't exist in the base file, the full URI is used. How can I add the prefix definition?