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These instructions are under construction. |
These instructions are for end users. With these instructions you can install cTAKES, configure it, and use it to process text (typically text associated with a medical record). If you were planning to expand, change, or modify the code within cTAKES, refer to the cTAKES 3.0 Developer Guide.
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Annotator | Description | Abbreviated | Example Aggregate Analysis Engine (AE) | Example Collection processing Engine (CPE) Example test data | |
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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/test1.xml | cTAKES_HOME/testdata/cdptest |
Chunker | obtain cTAKES chunking chunk annotations | chunker | NA | NA | |
Dependency Parser | obtain dependency parsing tree | dependency | cTAKES_HOME/desc/ctakes-chunkerdependency-parser/desc/analysis_engine/ChunkerAggregateClearParserSRLTokenizedInfPosAggregate.xml | cTAKES_HOME/desc/ctakes-dependency-chunkerparser/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 |
collection_processing_engine/ClearParserTestCPE.xml | |||||
Drug 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 dictionary | 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 NA |
PAD Term Spotter | identifying terms related to PAD | pad padtermspotter | 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 | relation-extractor | cTAKES_HOME/testdata/padtest/desc/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml | N/A | |
Smoking Status | the annotator to obtain document or patient-level smoking status smoking | smokingstatus | 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/collection_processing_engine/SideEffectCPE.xml cTAKES_HOME/testdata/sideeffecttest |
Next Steps
The cTAKES 3.0 Component Use Guide will help you to understand, in great detail, each of the cTAKES components that have been installed. In some cases you can learn how to improve the components.
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