The Default Clinical Pipeline is a great place for the new user of a binary installation 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.

On the command line run:

bin/runClinicalPipeline -i inputDirectory --htmlOut outputDirectory --key _umlsPasskey

There will be html files in your output directory that display the note text with underlines and other indications of discovered entities and their attributes.

If runClinicalPipeline fails with "ERROR PipelineBuilder - No Collection Reader specified.", verify that you used -i inputDirectory

The command line bin/runClinicalPipeline runs the Piper File DefaultFastPipeline.piper in resources/org/apache/ctakes/clinical/pipeline/