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From Christopher Li <chri...@augmedix.com>
Subject Question about using assertion module
Date Tue, 08 Sep 2015 22:10:09 GMT

I am a new user of cTAKES and would like to build a simple hello world type
application in Java that uses the assertion module.  It looks like a good
starting point is the ExampleAggregatePipeline class.  I modified line 46
in ExampleAggregatePipeline.java to print out the polarity as follows:

//Run the Aggregate Pipeline

SimplePipeline.runPipeline(jcas, builder.createAggregateDescription());

//Print out the IdentifiedAnnotation objects

for(IdentifiedAnnotation entity : JCasUtil.select(jcas,
IdentifiedAnnotation.class)){      System.out.println("Entity: " +
+ " === Polarity: " + entity.getPolarity());

However, for an assignment of *"Patient has fx of coronary artery disease" *to
the variable note the printed output is the following.  If I am not
mistaken, the phrase "coronary artery disease" was not detected as a single
named entity.  I was wondering what I may need to adjust within the example
code to change this behavior; for example, it seems like it may be
necessary for me to use a tokenizer that can perform UMLS lookup.

I would sincerely appreciate any feedback.

08 Sep 2015 15:05:48  INFO ExampleHelloWorldAnnotator - Token:Patient POS:NN

08 Sep 2015 15:05:48  INFO ExampleHelloWorldAnnotator - Token:artery POS:NN

08 Sep 2015 15:05:48  INFO ExampleHelloWorldAnnotator - Token:disease POS:NN

Entity: Patient === Polarity: 0

Entity: artery === Polarity: 0

Entity: disease === Polarity: 0


Christopher Li
Data Scientist, Augmedix
E-mail: chrisli@augmedix.com
Phone: 973-420-8243

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