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The Default Clinical Pipeline produces the most commonly desired output from cTAKES.  This includes annotations for Anatomical sites, Signs/Symptoms, Procedures, Diseases/Disorders and Medications.  For each annotation there are normalized UMLS CUIs, plus values for negation, uncertainty and subject.

Figure 1.  A sample sentence processed by the Default Clinical Pipeline.

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Run via command line.

1. Execute bin/runClinicalPipeline  -i inputDirectory  --xmiOut outputDirectory  --user umlsUsername  --pass umlsPassword

The pipeline will write log information to the screen and will write an XMI file for each file in inputDirectory and its subdirectories.  The directory tree below inputDirectory will be mirrored in outputDirectory.

You can view information in the XMI files using the UIMA Cas Visual Debugger (CVD). See the cTAKES 4.0 Component Use Guide for reference.

1. Execute bin/runctakesCVD
2. Select File > Read Type System File
3. Select TypeSystem.xml in resources/org/apache/ctakes/typesystem/types/
4. Select File > Read XMI CAS File
5. Select any .xmi file in your outputDirectory

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