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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject Re: Analyzing and processing cTakes NLP output
Date Wed, 09 Oct 2013 11:24:12 GMT
Hi Paula,
The typical way we visually inspect this information is in the CVD tool. Then for more systematic
access and processing we usually will write java code around an annotator that will use the
ctakes API and typesystem to extract what we need. Looking directly at the xml is usually
about as useful as you seem to have found it (i.e., not very :) ).

What task are you trying to accomplish? If you just want to see what concepts are found for
one file at a time that can be done in the CVD. If you are having trouble finding what you
need there let us know. If you want an output file with all terms that were listed in any
given input file that would probably require a little bit of programming.


On 10/08/2013 09:49 PM, digital girl wrote:
Hi Team (or is it just the Team of Samir ;-)

I had processed a 2 1/2 page narrative from the CVD tool and exported to XCAS file in xml.
  I would like to extract the key items from the narrative that cTakes is known for such as
identifying diseases/disorders, medications, signs/symptoms, and so forth.    I quickly perused
the file via xml browser and did see the SNOMED and RXNORM codes associated.   I decided to
printout out the file to markup the sections and to get an idea of how these codes relate
back to the concepts identified by cTakes.   My printer ran out of paper after about 60 pages
and when I looked at the top sheet it was 1 out of 2243 pages!   A 2 1/2 page narrative resulted
in an xml file of over two thousand pages!!!

 I examined the first medication mapping.  The numeric lines are my comments and everything
else copy/pasted from XCAS file.

1.  Identification of RxNorm code is 69749 but it's not associated with a concept so I copied
'163573' and pasted in search in the xml file.   See number 2 below for what retrieved.
<uima.cas.FSArray _id="163573" size="1">
<org.apache.ctakes.typesystem.type.refsem.OntologyConcept _id="163539" codingScheme="RXNORM"
code="69749" oid="69749#RXNORM"/>

2.  Retrieved this result with some additional information such as the generic is false, 
but not med name mention.  I  copied "163581" and pasted in search.  See number 3 below for
what retrieved.
_indexed="1" _id="163581" _ref_sofa="6" begin="9776" end="9784" id="530" _ref_ontologyConceptArr="163573"
typeID="1" segmentID="SIMPLE_SEGMENT" discoveryTechnique="1" confidence="1.0" polarity="1"
uncertainty="0" conditional="false" generic="false" subject="patient" historyOf="0"/>

3.  Retrieved this result.  The RxNorm code associated identifies Coumadin as a treatment.
<org.apache.ctakes.assertion.medfacts.types.Concept _indexed="1" _id="227307" _ref_sofa="6"
begin="9776" end="9784" conceptType="TREATMENT" conceptText="Coumadin" externalId="0" originalEntityExternalId="163581"/>

Here are my questions:

1. is there any resources available that explains what the xml output file contains and the
layout?  Such as what does confidence of 1.0 and polarity of 1 and uncertainty of 0 refer

2.  Are there any tools already existing that interpret the NLP output from cTakes and automatically
structure and associate it to the concepts?  Such as, automatically associate the RxNorm to
the medication mention as illustrated above.   As you see it took a few steps to associate
the RxNorm code to the actual medication mention from the narrative.



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