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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:
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.