Add Clingen subset to release products #8530
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Suprising that was never noticed: the SUBSETDIR variable used here was never declared..
Basically, take the labels, and swap them out for clingen preferred labels
| } | ||
| FILTER NOT EXISTS { | ||
| ?cls owl:deprecated "true"^^xsd:boolean | ||
| } |
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Should obsolete terms be excluded? There are obsolete Mondo terms that have the clingen subset annotation. Is there some other way that ClinGen is notified of obsolete Mondo terms in the clingen subset?
Edit: Although after running the new goal (sh run.sh make subsets/mondo-clingen.owl -B) obsolete terms in the clingen subset are in mondo-clingen.owl.
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Is there some other way that ClinGen is notified of obsolete Mondo terms in the clingen subset?
The primary way some people in clingen learn of this is through:
and
They read those files with every release and supposedly generate curation instructions based on these.
Edit: Although after running the new goal (sh run.sh make subsets/mondo-clingen.owl -B) obsolete terms in the clingen subset are in mondo-clingen.owl.
Hmm.. Both questions (why is it in and should it be in) are good questions we need to answer in an upcoming meeting.
| owl:annotatedSource ?entity ; | ||
| owl:annotatedProperty oboInOwl:hasExactSynonym ; | ||
| owl:annotatedTarget ?label ; | ||
| oboInOwl:hasSynonymType <http://purl.obolibrary.org/obo/mondo#MONDO_LABEL> . |
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This http://purl.obolibrary.org/obo/mondo#MONDO_LABEL does not exist as a synonym_type_property.
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Yes, there is no synonym type for that "idea" (the "label" used in Mondo). This is an ad-hoc synonym type just for this subset!
And do a bit of SUBSETDIR refactoring in the Makefile.