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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/cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml | cTAKES_HOME/cTAKESdesc/cdpdesc/collection_processing_engine/test_plaintext.xml | cTAKES_HOME/testdata/cdptest |
Chunker | obtain cTAKES chunking annotations | chunker | cTAKES_HOME/cTAKESdesc/chunkerdesc/analysis_engine/ChunkerAggregate.xml | cTAKES_HOME/cTAKESdesc/chunkerdesc/collection_processing_engine/ChunkerCPE.xml | cTAKES_HOME/testdata/chunkertest |
Dependency Parser | obtain dependency parsing tree | dp | cTAKES_HOME/cTAKESdesc/dpdesc/analysis_engine/ClearParserTokenizedInfPosAggregate.xml | cTAKES_HOME/cTAKESdesc/dpdesc/collection_processing_engine/ClearParserCPE.xml | cTAKES_HOME/testdata/dptest |
Drug NER | the annotator to obtain drug annotations | drugner | cTAKES_HOME/cTAKESdesc/drugnerdesc/analysis_engine/DrugAggregatePlaintextProcesor.xml | cTAKES_HOME/cTAKESdesc/drugnerdesc/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/cTAKESdesc/lookupdesc/analysis_engine/TestAggregateTAE.xml | cTAKES_HOME/cTAKESdesc/lookupdesc/collection_processing_engine/LookupCPE.xml | cTAKES_HOME/testdata/lookuptest |
PAD Term Spotter | identifying terms related to PAD | pad | cTAKES_HOME/cTAKESdesc/paddesc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml | cTAKES_HOME/cTAKESdesc/paddesc/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/cTAKESdesc/smokingdesc/analysis_engine/SimulatedProdSmokingTAE.xml | cTAKES_HOME/cTAKESdesc/smokingdesc/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/cTAKESdesc/sideeffectdesc/analysis_engine/SideEffectAggregateTAE.xml | cTAKES_HOME/cTAKESdesc/sideeffectdesc/collection_processing_engine/SideEffectCPE.xml | cTAKES_HOME/testdata/sideeffecttest |
Next Steps
The cTAKES 23.6 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. However, before you go on to process text in production you will need to consider dictionaries and models.
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Some models included in cTAKES may not represent your data distribution well. If you want to build or train your own models, please read the cTAKES 23.6 0 Component Use Guide, particularly:
- Training a sentence detector model
- Training a Part of Speech (POS) tagger model (Building a model Obtaining training data)
- Creating a Part of Speech (POS) tag dictionary (Building a tag dictionary)
- Training a chunker model (Building a model - Prepare GENIA training data)
- Training a dependency parser (Dependency Parser)