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Overview of Clinical Documents Pipeline

This project is the top-level, main project for processing a clinical document through the entire cTAKES pipeline, including sentence detection, part of speech tagging POS, chunking, named entity recognition, context detection, and negation detection.

The pipeline can process two types of documents

• plain text files
• Clinical Document Architecture (CDA) XML files that conform to the DTD provided

Analysis engines (annotators)

AggregateCdaProcessor.xml for CDA documents conforming to the provided DTD

The file desc/analysis_engine/AggregateCdaProcessor.xml is the aggregate analysis engine to use to run the entire pipeline, including the CdaCasInitialzer analysis engine, which reads CDA documents that conform to the DTD provided, and create Segment annotations based on the sections within the CDA document.

Parameters

ChunkerCreatorClass - the full class name of an implementation of the interface edu.mayo.bmi.uima.chunker.ChunkerCreator

AggregatePlaintextProcessor.xml for plain text documents

The file desc/analysis_engine/AggregatePlaintextProcessor.xml is the aggregate analysis engine to use to run the entire pipeline, including the SimpleSegmentAnnotator analysis engine, which creates a Segment annotation that wraps the entire plain text document. Other annotators in the pipeline require at least one Segment annotation.

Parameters

SegmentID - the identifier or name to assign to the Segment annotation
ChunkerCreatorClass -  the full class name of an implementation of the interface edu.mayo.bmi.uima.chunker.ChunkerCreator