THIS IS A TEST INSTANCE. ALL YOUR CHANGES WILL BE LOST!!!!
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This version allows you to test most components bundled in cTAKES in two different the following ways:
- Using the bundled UIMA CAS Visual Debugger (CVD) to run a pipeline and view the results. Also allows you to view the results stored that have been saved as XCAS files or run the annotators
- Using the bundled UIMA Collection Processing Engine (CPE) to process documents in cTAKES_HOME/testdata directoryin a directory and save the results in another directory.
- Using the cTAKES 4.0 GUI
On Linux, you will need a windowing environment to run these tools.
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The cTAKES GUI can be launched using bin\runctakesGUIrunPiperCreator.bat or bin\runctakesGUIrunPiperCreator.sh
Step 1: Open a command prompt and change to the cTAKES_HOME directory, which is the directory that contains subdirectories like bin, desc, resources, lib.
Step 2 for Windows: bin\runctakesGUIrunPiperCreator.bat
Step 2 for Linux: bin\runctakesGUIrunPiperCreator.sh
Step 3: Allow the GUI to scan for annotators
Step 4: Select which elements to include in your pipeline
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The analysis engines and collection processing engines shipped with cTAKES for some of the annotators are described in the following table.
| Warning |
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TBD - TODO - fix this - cTAKES 3.1 binary distributions did not include test data. Loading the CPE descriptors into the CPE tool will require resetting the input and output directories. Test files could be obtained from the cTAKES 2.5 release binary distribution. Look for a testdata directory in cTAKES_HOME. |
Annotator | Description | Example Piper file | ||
|---|---|---|---|---|
Clinical | ||||
Annotator | Description | Example Piper file | Example Collection processing Engine (CPE) | |
Clinical Pipeline | The pipeline to obtain concepts and their attributes | <cTAKES_HOME>/TBD | <cTAKES_HOME>/TBD<cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml | |
Chunker | Obtains phrasal chunk annotations | <cTAKES_HOME>/TBDNA | ||
Dependency Parser | Obtains dependency parsing tree | <cTAKES_HOME>/TBD<cTAKES_HOME>/desc/ctakes-dependency-parser/desc/collection_processing_engine/ClearParserTestCPE.xml | ||
Drug NER | Finds mentions of medications and medication attributes such as dose, strength, frequency... <cTAKES_HOME>/TBD | <cTAKES_HOME>/desc/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml/TBD | ||
Dictionary Lookup | Finds mentions of concepts from a dictionary (e.g., SNOMED CT or RxNorm | <cTAKES_HOME>/TBDNA | ||
Dictionary Lookup Fast | Finds mentions of concepts from a dictionary (e.g., SNOMED CT or RxNorm | <cTAKES_HOME>/TBDNA | ||
Relation Extractor | Finds certain relations (location of and degree of) between certain Event, Entity, and Modifier annotations | <cTAKES_HOME>/TBDN/A | ||
Smoking Status | Finds document or patient-level smoking status | <cTAKES_HOME>/TBD<cTAKES_HOME>/desc/ctakes-smoking-status/desc/collection_processing_engine/Sample_SmokingStatus_output_flatfile.xml | ||
Side Effect | Finds side effect mentions and sentences from clinical documents | <cTAKES_HOME>/TBD<cTAKES_HOME>/desc/ctakes-side-effect/desc/collection_processing_engine/SideEffectCPE.xml |
Next Steps
The cTAKES 4.0 Component Use Guide will help you to understand each of the cTAKES components that have been installed. In some cases you can learn how to improve the components.
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