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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Temporal module dictionary
Date Thu, 11 May 2017 17:39:22 GMT
Hi Erin,
Can you make a call to OntologyConceptUtil.getCuis( jcas ).forEach( System.out::println )
at the end of your pipeline?  If any of the cuis are outside your dictionary then it is using
some other source to get them.  If not then you are getting non-dictionary events marked.
 Alternatively you could use the EntityCollector and/or CuiCollector singletons.

If you don't want to write extra code then add one of the following cas consumers from core
to the end of your pipeline:
  CuiCountFileWriter
  pretty.plaintext.PrettyTextWriterFit
  pretty.html.HtmlTextWriter

Sean


-----Original Message-----
From: Erin Gustafson [mailto:erin.gustafson@northwestern.edu] 
Sent: Thursday, May 11, 2017 12:59 PM
To: dev@ctakes.apache.org
Subject: RE: Temporal module dictionary

Correct!


-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu] 
Sent: Thursday, May 11, 2017 11:57 AM
To: dev@ctakes.apache.org
Subject: RE: Temporal module dictionary

Hi Erin,

So, just to be clear, you changed line #110 in TemporalExtractionPipeline_ImplBase, the getFastPipeline()
method from:
    builder.add( DefaultJCasTermAnnotator.createAnnotatorDescription() );
to:
    builder.add( DefaultJCasTermAnnotator.createAnnotatorDescription( path/to/my/config.xml
) );

Is that correct?

Thanks,
Sean 

-----Original Message-----
From: Erin Gustafson [mailto:erin.gustafson@northwestern.edu] 
Sent: Thursday, May 11, 2017 12:44 PM
To: dev@ctakes.apache.org
Subject: Temporal module dictionary

Hi all,

I would like to use the temporal module to detect temporal relations involving events specific
to a phenotype. I've created a custom .bsv dictionary with a limited set of concepts relevant
to that phenotype, which I have used in the past as input to the dictionary look-up algorithm.
Now I'd like to try to use the same dictionary with the temporal module to limit the extracted
relations to those involving events of interest.

Is it possible to do this? I've plugged my dictionary in to FullTemporalExtractionPipeline,
but the detected events still include concepts that fall outside my dictionary.

Thanks,
Erin

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