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Annotator

Description

Abbreviated

Example Analysis Engine (AE)

Example Collection processing Engine (CPE)

Example test data

Clinical Document Pipeline

the complete cTAKES pipeline to obtain majority of cTAKES annotations

cdp

cTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml

cTAKES_HOME/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml

cTAKES_HOME/testdata/cdptest

Chunker

obtain cTAKES chunking annotations

chunker

cTAKES_HOME/desc/ctakes-chunker/desc/ChunkerAggregate.xml

cTAKES_HOME/desc/ctakes-chunker/desc/ChunkerCPE.xml

cTAKES_HOME/testdata/chunkertest

Dependency Parser

obtain dependency parsing tree

dp

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

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

cTAKES_HOME/testdata/dptest

Drug NER

the annotator to obtain drug annotations

drugner

cTAKES_HOME/desc/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcesor.xml

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

cTAKES_HOME/testdata/drugnertest

Dictionary Lookup

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

lookup

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

cTAKES_HOME/desc/ctakes-dictionary-lookup/desc/collection_processing_engine/LookupCPE.xml

cTAKES_HOME/testdata/lookuptest

PAD Term Spotter

identifying terms related to PAD

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

cTAKES_HOME/testdata/padtest

Smoking Status

the annotator to obtain document or patient-level smoking status

smoking

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

cTAKES_HOME/testdata/smokingtest

Side Effect

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

sideeffect

cTAKES_HOME/desc/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE.xml

cTAKES_HOME/desc/ctakes-side-effect/desc/cpecollection_processing_engine/SideEffectCPE.xml

cTAKES_HOME/testdata/sideeffecttest

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