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[bioontology-support] Prefix to call Annotator

Ray Fergerson ray.fergerson at
Fri May 24 17:12:34 PDT 2013

However, I still have one question: I want to set the parameter
longestOnly=true, but I received an error message stating that I cannot do
it if either "ontologiesToExpand" or "ontologiesToKeepInResult" is
populated. Since I would rather receive the response with just a few
ontologies, is there any way I can do this?


Unfortunately there is an architectural issue that prevents us from fixing
this problem. The third-party library that we use that does concept
recognition and detects “longest only” works over all terms in all
ontologies – it doesn’t really know about ontologies. The ontology
filtering is done after the fact. This means that the “longest” terms
detected by the library may be removed by filtering and no term at all
returned to the user. There is no good way to fix this without
reimplementing longest only detection outside the library. We may
eventually do this but it is not a high priority. For the moment you need
to filter on your side.


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