RE: How to replace SubjectCleartkAnalysisEngine with SubjectAttributeAnalysisEngine in ClinicalPipelineFactory.java

["Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>]

Hi Yiming,

Did you ever succeed in getting a "conditional" attribute annotator to work? I need the same thing, and like you it seems that ClearTK isn't doing anything for me for the conditional attribute.

Thanks,
Sean

-----Original Message-----
From: Zuo Yiming [mailto:yimingzuo@gmail.com] 
Sent: Wednesday, March 15, 2017 12:30 PM
To: dev@ctakes.apache.org
Subject: How to replace SubjectCleartkAnalysisEngine with SubjectAttributeAnalysisEngine in ClinicalPipelineFactory.java

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