How to replace SubjectCleartkAnalysisEngine with SubjectAttributeAnalysisEngine in ClinicalPipelineFactory.java

[Zuo Yiming]

Hi everyone,

Earlier I shared my experience with the community about which analysis
engines used together can work better to identify negation, history,
uncertainty, subject, etc. ClearTk didn't work for me to detect subject,
generic and conditional status, while SubjectAttribute and GenericAttribute
worked fine.

I'm now trying to modify ClinicalPipelineFactory.java to
replace SubjectCleartkAnalysisEngine and GenericCleartkAnalysisEngine with
SubjectAttributeAnalysisEngine and GenericAttributeAnalysisEngine in
getFastPipeline method. However, it seems SubjectAttributeAnalysisEngine
and GenericAttributeAnalysisEngine doesn't have the
createAnnotatorDescription methods, which I hope I can put into
builder.add(). Can anyone guide me how to move on? Or maybe there're
additional parameters to provide to ClearTk in order to make it work
properly to detect subject, generic and conditional status?

Below are the getFastPipeline method in ClinicalPipelineFactory.java where
I believe the change should be made:

public static AnalysisEngineDescription getFastPipeline() throws
ResourceInitializationException, MalformedURLException {
      AggregateBuilder builder = new AggregateBuilder();
      builder.add( getTokenProcessingPipeline() );
      builder.add( DefaultJCasTermAnnotator.createAnnotatorDescription() );
      builder.add( ClearNLPDependencyParserAE.createAnnotatorDescription()
);
      builder.add(
PolarityCleartkAnalysisEngine.createAnnotatorDescription() );
      builder.add(
UncertaintyCleartkAnalysisEngine.createAnnotatorDescription() );
      builder.add(
HistoryCleartkAnalysisEngine.createAnnotatorDescription() );
      builder.add(
ConditionalCleartkAnalysisEngine.createAnnotatorDescription() );

-----------------------------------------------------------------------------------------------------
      builder.add(
GenericCleartkAnalysisEngine.createAnnotatorDescription() );
      builder.add(
SubjectCleartkAnalysisEngine.createAnnotatorDescription() );

---------------------------------------------------------------------------------------------------
      return builder.createAggregateDescription();
   }

Thanks,
Yiming