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[bioontology-support] Populating ontologies on NCBO virtual appliance, and filtering annotator results

Colin Morris colin at sciencescape.org
Wed Mar 20 09:48:42 PDT 2013


Hi,

We're interested in using the NCBO annotator in an application of ours.
Because we have millions of short documents that we'd like to annotate, we
thought we'd run the virtual appliance locally (to speed things up on our
end, and avoid imposing on your servers too much).

I was (maybe naively) expecting that the image would include the same
ontologies as on bioportal.bioontology.org. Is there an easy way to
reproduce something like that environment locally? That is, easier than
locating each of the ~335 ontologies currently on the site and adding them
through the web interface? (We'd like to cast as broad a net as possible)

Or, given a copy of the most recent release of the UMLS (which we have), is
there an easy way to plug it into our local NCBO instance? (I see there's a
way to add RRF files as ontologies, but there are 42 associated with our
UMLS install, and I suspect that just dropping them all in won't have the
desired effect.)


And a mostly unrelated question: Given the results of a call to the
Annotator web service, is there any way to get the UMLS CUI of each
returned concept? I see that the concept element has an 'id' and a
'localconceptid', but neither of those seem to correspond to UMLS.

I see that the annotator has the option to expand its results to infer new
results that have the same CUI as found concepts. What I'd like to do is
the opposite -- get distinct concepts, by CUI.

Any help very much appreciated!

Thanks,
Colin
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