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Using the same CVD and CPE programs in the manner described above, you can test all the other components. The analysis engines and collection processing engines shipped with cTAKES for some of the annotators are described in the following table.
| Warning |
|---|
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. |
Annotator | Description Abbreviated | Example Aggregate Analysis Engine (AE) | Example Collection processing Engine (CPE) | |
|---|---|---|---|---|
Clinical Document Pipeline | the The complete cTAKES pipeline to obtain majority of cTAKES annotations | cdp | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml |
Chunker | obtain Obtain cTAKES chunk annotations | chunker | NA | NA |
Dependency Parser | obtain Obtain dependency parsing tree | dependency | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedInfPosAggregate.xml | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-dependency-parser/desc/collection_processing_engine/ClearParserTestCPE.xml |
Drug NER | the The annotator to obtain drug annotations | drugner | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcesor.xml | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml |
Dictionary Lookup | mapping Mapping cTAKES annotations to dictionaries (e.g., SNOMED_CT or RxNorm | dictionary | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-dictionary-lookup/desc/analysis_engine/TestAggregateTAE.xml | NA |
PAD Term Spotter | identifying Identifying terms related to PAD | padtermspotter | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_Sample.xml |
Relation Extractor | annotate Annotate certain relations between certain Event, Entity, and Modifier annotations | relation-extractor | cTAKES_HOME <cTAKES_HOME>/desc/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml | N/A |
Smoking Status | the The annotator to obtain document or patient-level smoking status | smokingstatus | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-smoking-status/desc/collection_processing_engine/Sample_SmokingStatus_output_flatfile.xml |
Side Effect | the The annotator to find side effect mentions and sentences from clinical documents | sideeffect | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE.xml | cTAKES <cTAKES_HOMEHOME>/desc/ctakes-side-effect/desc/collection_processing_engine/SideEffectCPE.xml |
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