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These instructions are for end users. With these instructions you can install Apache 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 3.1 Developer Install Guide.
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Step | Example | |||||||||||||||||
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1. Navigate to the cTAKES downloads page on the Apache site and download the binary package. Select a mirror site and press the Change button to modify the URL to your desired mirror location before doing the download or accept the default.
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2. (Optional but recommended) Verify the downloaded files against a file signature to ensure you have the proper and complete file. | No example | |||||||||||||||||
3. Unzip the file you downloaded into a directory that you want to be the cTAKES install location. The compressed files contain a single directory at the top level. This folder we will call <cTAKES_HOME>. You will need to refer to this directory later.
Linux:
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4. Download the cTAKES resources ZIP file with a matching version from the ctakesresources project (More information on cTAKES models). These resources are required to operate cTAKES.
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5. Copy (or move) the resources to cTAKES_HOME.
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Linux:
Mac OSX:
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Step | Example | ||||||||||||
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1. Open a command prompt and change to the cTAKES_HOME directory.
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Linux:
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2. Start the CAS Visual Debugger by running this command: | Windows:
Linux:
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3. Copy the example text from the next cell in this table and paste the contents into the Text section of CVD, replacing the text that is already there. |
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4. An analysis engine (AE) needs to be loaded in order to process text.
rather than
in this step.
Click Open.
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5. From the menu bar, click Run -> Run AggregatePlaintextProcessor or "Run AggregatePlaintextUMLSProcessor". | |||||||||||||
6. You'll get a list of all the annotations for this clinical document in the Analysis Results frame. Annotations such as named entities, division by sentence, etc from the pipeline are viewable. To see one, in the Analysis Results frame, click on the key in front of:
This will show an AnnotationIndex in the lower frame. Select any annotation in that lower frame and you will see the text discovered in
Now select items in the lower frame to see the text being annotated. |
Collection Processing Engine (CPE)
Step | Example | ||||||||||||
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1. Open a command prompt and change to the cTAKES_HOME directory:
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Linux:
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2. Create a directory for some test data. | Windows:mkdir testdata | ||||||||||||
3. Download this sample file and place it into the testdata directory. | No example | ||||||||||||
4. Start the collection processing engine by running this command: | Windows:
Linux:
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5. This will bring up the Collection Processing Engine Configurator. In the Menu bar click File >Open CPE Descriptor | |||||||||||||
6. Navigate to the following file, which uses the AggregateCdaProcessor
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7. Change the Collection reader input directory to testdata, which contains a CDA file(s). | |||||||||||||
8. Click the Play button (green/blue play arrow near the bottom).
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9. You should see that one document was processed. You did process a collection of documents. In this case the collection only contained one just to show how to do it. Close the results window.
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10. Close the CPE application. You may be prompted to save changes. Since this was just a test you may click the No button. | No example |
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.
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Annotator | Description | Example Aggregate Analysis Engine (AE) | Example Collection processing Engine (CPE) |
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Clinical Document Pipeline | The complete cTAKES pipeline to obtain majority of cTAKES annotations | <cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.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/DrugAggregatePlaintextUMLSProcesor.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_UMLS.xml | <cTAKES_HOME>/desc/ctakes-side-effect/desc/collection_processing_engine/SideEffectCPE.xml |
Next Steps
The cTAKES 3.1 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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