Hello,
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: " +
entity.getCoveredText()
+ " === 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
-Chris
--
Christopher Li
Data Scientist, Augmedix
E-mail: [email protected]
Phone: 973-420-8243
