Feature request: Option to exclude obsolete classes from results

[matentzn]

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 Example: this query returns http://purl.obolibrary.org/obo/FBbt_00002047, which is obsolete.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]

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

[balhoff]

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.