Hi cTAKES Team,

I've recently started exploring cTAKES and I'm excited about the potential.
However, I'm having trouble seeing the results as they're exemplified in
the documentation using the example input "The patient underwent a CT Scan
in April which did not reveal lesions in his liver."

Specifically negation (polarity) values don't seem to be populated as they
are shown in the Default Clinical Pipeline documentation wiki page
<https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline>.
I've built a simple java class which instantiates the Default Pipeline like
so

static AnalysisEngine pipeline;

…

log.info( "Initilizing Pipeline..." );


try

{

  AggregateBuilder builder = new AggregateBuilder( );

  builder.add( ClinicalPipelineFactory.getDefaultPipeline( ) );

     pipeline = builder.createAggregate( );

}

catch( Exception e )

{

  log.error( e );

}

…


I then instantiate a CAS and process it like so:


try

{

  JCas jcas = pipeline.newJCas( );

  jcas.setDocumentText( "The patient underwent a CT Scan in April which did
not reveal lesions in his liver." );

  pipeline.process( jcas );

}

catch( Exception e )

{

  log.error( e );

}

…


I've set my UMLS username and password as environment variables, and UMLS
lookups are working just fine. The CAS contains the same identified
annotations as the example, i.e. The AnatomicalSiteMentions,
SignSymptomMentions, etc, however, the fields for polarity are all 1. The
documentation on the wiki page for Assertion Component Use Guide
<https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Assertion>,
and the aforementioned wiki page for the default clinical pipeline lead me
to think that the polarity field for the 'lesions' concept would be set to
1, and leave the rest -1.


Is there something I'm missing? Perhaps I'm not looking in the right place,
or haven't done all of the configuration required to exercise those
features of cTAKES?


I've attached the serialized CAS object to this email for reference.




Best,

Chris


-- 
Chris Hinkle
All Turtles
347-407-4993
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