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1. Open a command prompt and change to the cTAKES_HOME directory, which is the directory that contains subdirectories like bin, desc, resources, lib. Depending on how you extracted the files,
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Linux:
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2. This step uses AggregatePlaintextFastUMLSProcessor, which requires that you downloaded the cTAKES resources as described in step 4 of Install cTAKES (above) and that you added UMLS access rights (also above). If you haven't done those, you can use the AggregatePlaintextProcessor instead. Start the CAS Visual Debugger and load the AggregatePlaintextFastUMLSProcessor pipeline by running this command (at right)
The GUI opens and then loads the AggregatePlaintextFastUMLSProcessor pipeline. If it appears to be hung, look at the window where you entered the command and you will see what is happening. Once the analysis engine has successfully loaded you should see a tree in the Analysis Results frame:
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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. From the menu bar, click Run -> Run AggregatePlaintextFastUMLSProcessor. Note: If you would like to TEST some simple annotators to ensure it's working without UMLS, you can just load: /desc/ctakes-core/desc/analysis_egine/SentencesAndTokensAggregate.xml |
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5. 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. |
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To run other pipelines, use the Run-> Load AE menu bar command. Navigate to the file you wish to load, such as
Click Open.
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