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From "Tonner, Chris" <Chris.Ton...@ucsf.edu>
Subject cTakes - help please
Date Mon, 19 Oct 2015 21:38:31 GMT
Hello:

I work in the Department of Medicine at the University of California, San Francisco.  We are
interested in cTakes to extract medical information from our EMRs.

I have been attempting to install and run cTakes, but have had some problems.  Would you be
able to give us technical help to get cTakes up and running.

Following the instructions on the User Installation Guide.   https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+User+Install+Guide

I  have modified the two bat files c: bin\runctakesCVD.bat file  and CPE.bat... Example of
modified code - is this correct?

@REM set ctakes.umlsuser=[christonner], ctakes.umlspw=[123Start]
@REM or add the properties
@REM -Dctakes.umlsuser=[christonner] -Dctakes.umlspw=[123Start]

These batch files run and the debugger opens.

I can load some of the analysis engine, but get errors with the UMLS and the negation AE.

In short we are at a loss on how to troubleshoot this.  Is there a more extensive manual on
how to install cTakes and how to use cTakes?

Error Examples.

SEVERE: Malformed URL c:/apache-ctakes-3.2.2/des/ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml
in import declaration. (Descriptor: file:/C:/apache-ctakes-3.2.2/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml)
org.apache.uima.resource.ResourceInitializationException: Malformed URL c:/apache-ctakes-3.2.2/des/ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml
in import declaration.
(Descriptor: file:/C:/apache-ctakes-3.2.2/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml)
[cid:image001.png@01D10A7A.C42CE720]

Thanks you,
Chris Tonner
University of California, San Francisco




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