subject attribute in EntityMention element

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Jason

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Dec 11, 2012, 4:21:51 PM12/11/12
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In plain cTAKES using the AggregatePlainTextUMLSProcessor, the EntityMention elements in the XML output files have "subject" attributes, which can be valued as "patient" or "family_member".  However, using ytex with the YTEXMetaMapClinicalPipeline, the EntityMention elements do not have subject attributes.  Based on my investigations, I have guessed that the subject attributes are produced by the SubjectAttributeAnalysisEngine in the AssertionMiniPipelineAnalysisEngine.  I made a sort of naive attempt to add the AssertionMiniPipelineAnalysisEngine to the YTEXMetaMapClinicalPipeline, but the resulting pipeline just hangs and never processes any records.  I also tried including just the SubjectAttributeAnalysisEngine, which gives me an error message:

org.apache.uima.analysis_engine.AnalysisEngineProcessException: Annotator processing failed. 
CausedBy: java.lang.ArrayIndexOutOfBoundsException: -1

I'm attaching the pipeline I created with the SubjectAttributeAnalysisEngine.  Perhaps I made some kind of rookie mistake.
Is there anybody here who can give me any advice on this problem?  My goal is to be able to run a clinical pipeline that includes MetaMap and produces EntityMention elements with subject attributes.

Best,

Jason





YTEXSubjectMetamapPipeline.xml
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