phenoscape/owlery

Feature request: Option to exclude obsolete classes from results

matentzn opened this issue · 2 comments

matentzn commented

At the moment, owlery returns obsolete classes as part of their responses. It would be great (and for applications probably necessary) to be able to exclude those. Example: this query returns http://purl.obolibrary.org/obo/FBbt_00002047, which is obsolete.

balhoff commented

This is implemented in master now. Use includeDeprecated=false (default is true).

balhoff commented

This depends on performance of OWL API to search for annotations here:

owlery/src/main/scala/org/phenoscape/owlery/Knowledgebase.scala

Line 134 in 5b97d2f

EntitySearcher.getAnnotations(entity, o, factory.getOWLDeprecated).asScala.exists { v =>

I don't know if they have an index, or it just scans through. If that is slow for some reason, we can make an index of deprecated classes at startup.