The Default Clinical Pipeline is a great place for the new user of a binary installation to start. New developers should look at the ctakes-examples
project to start.
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.
Step-by-step guide
Run via command line.
- 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).
- Execute bin/runctakesCVD
- Select File > Read Type System File
- Select
TypeSystem.xml
inresources/org/apache/ctakes/typesystem/types/
- Select File > Read XMI CAS File
- Select any
.xmi
file in youroutputDirectory
Selections in the tree on the left can provide highlighting in the document text on the right. Browsing annotations is not necessarily straightforward. Reference the CVD main area documentation if necessary.
The command line bin/runClinicalPipeline runs the Piper File DefaultFastPipeline.piper
in resources/org/apache/ctakes/clinical/pipeline/
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