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changes.mady.by.user Pei Chen

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changes.mady.by.user James Masanz

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Comment: remove PAD term spotter since it was no longer part of the distribution (was deprecated)

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Annotator

Description

Example Aggregate Analysis Engine (AE)

Example Collection processing Engine (CPE)

Clinical Document Pipeline

The complete cTAKES pipeline to obtain majority of cTAKES annotations

<cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml

<cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml

Chunker

Obtain cTAKES chunk annotations

NA

NA

Dependency Parser

Obtain dependency parsing tree

<cTAKES_HOME>/desc/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedInfPosAggregate.xml

<cTAKES_HOME>/desc/ctakes-dependency-parser/desc/collection_processing_engine/ClearParserTestCPE.xml

Drug NER

The annotator to obtain drug annotations

<cTAKES_HOME>/desc/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcesor.xml

<cTAKES_HOME>/desc/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml

Dictionary Lookup

Mapping cTAKES annotations to dictionaries (e.g., SNOMED_CT or RxNorm

<cTAKES_HOME>/desc/ctakes-dictionary-lookup/desc/analysis_engine/TestAggregateTAE.xml

NA

PAD Term Spotter

Identifying terms related to PAD

<cTAKES_HOME>/desc/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml

<cTAKES_HOME>/desc/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_Sample.xml

Relation Extractor

Annotate certain relations between certain Event, Entity, and Modifier annotations

<cTAKES_HOME>/desc/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml

N/A

Smoking Status

The annotator to obtain document or patient-level smoking status

<cTAKES_HOME>/desc/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml

<cTAKES_HOME>/desc/ctakes-smoking-status/desc/collection_processing_engine/Sample_SmokingStatus_output_flatfile.xml

Side Effect

The annotator to find side effect mentions and sentences from clinical documents

<cTAKES_HOME>/desc/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE_UMLS.xml

<cTAKES_HOME>/desc/ctakes-side-effect/desc/collection_processing_engine/SideEffectCPE.xml

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