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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject cTAKES doesn't pull spatial concepts
Date Mon, 08 Jul 2013 19:02:23 GMT

I was forwarded the question below. My reply, also below, provided enough information for
the problem to be solved, so the original questioner suggested I  share the question and reply
here:


<reply-snippet>

 Apache cTAKES is configured to annotate named entities only within certain semantic types
(that is, only concepts with certain UMLS TUI values)
So if "right occipital region"  is a UMLS concept  not within a semantic type cTAKES annotates,
at minimum, you need to add the semantic type(s) you want included to be within one of the
LookupDesc*xml files  (which one depends on which pipeline you are running)
For example, LookupDesc_Db.xml contains this line:
<property key="anatomicalSiteTuis" value="T021,T022,T023,T024,T025,T026,T029,T030"/>
which shows that only those TUIs are considered when annotating anatomical sites

So it might be a case of adding a TUI to that list.

On the other hand it could just be either of these:
- maybe SNOMED-CT doesn't distinguish between left and right occipital regions?
- or maybe it does, but UMLS concepts do not - it is possible in such a case that 2 or more
SNOMED-CT terms map to a single UMLS concept if the SNOMED-CT terms are more specific.

Which leads to the question - specifically, which UMLS concept(s) were you expecting cTAKES
to find/return?

</reply-snippet>

<question-snippet>

I am using the CAS Visual Debugger to pull UMLS concepts out of my text using the AggregatePlaintextUMLSProcessor
analysis engine, and it works great.  However, I noticed that it doesn't pull spacial concepts
-- for instance, in the phrase "right occipital region" it only identifies "occipital region"
as a concept.  It would be nice to have the location and unique identifier for spacial concepts.
 Is there a place in the CVD gui to change the filters so that it picks up things like spacial
concepts?  Do I have to go with another analysis engine?

</question-snippet>




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