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| Warning |
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cTAKES 3.0 binary distributions did not include test data. Loading the CPE descriptors into the CPE tool will require resetting the input and output directories and obtaining valid test files. Test files could be obtained from the cTAKES 2.5 release binary distribution. Look for a testdata directory in cTAKES_HOME. |
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/AggregatePlaintextProcessor.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/DrugAggregatePlaintextProcesor.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.xml | <cTAKES_HOME>/desc/ctakes-side-effect/desc/collection_processing_engine/SideEffectCPE.xml |
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