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1. Open a command prompt and change to the cTAKES_HOME directory.
Windows:

cd \cTAKES-3.1

Linux:

cd /usr/bin/cTAKES-3.1

2. Start the CAS Visual Debugger by running this command:
Windows:

bin\runctakesCVD.bat

Linux:

bin/runctakesCVD.sh

The application may take a minute to start on slower hardware.

3. An analysis engine (AE) needs to be loaded in order to process text.
Use the Run-> Load AE menu bar command. Navigate to the file

<cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml

Click Open.
Loading the analysis engine may take a minute. When the analysis engine has successfully loaded you should see a tree in the Analysis Results frame:

Wiki Markup
CAS Index

Repository \\ \* SofaIndex \[0\] \\ \* AnnotationIndex \[1\] \\

4. Copy the text in the example at the right (next cell) and paste the
contents into the Text section of CVD, replacing the text that is
already there.
This example file can also be found in test data:

<cTAKES_HOME>/testdata/cdptest/testinput/plaintext/testpatient_plaintext_1.txt

Dr. Nutritious

Medical Nutrition Therapy for Hyperlipidemia

Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001
Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average intake of 1100 calories.
She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further assessment. May want a Resting
Metabolic Rate as well. She takes an aspirin a day for knee pain.

3. From the menu bar, click Run -> Run AggregatePlaintextProcessor.
You'll get a list of all the annotations in the Analysis Results frame.

4. Named entities are now recognized in this clinical document.
Annotations of MedicationEventMention and EntityMention are created. To
find one, in the Analysis Results frame, click on the key in front of:

CAS Index Repository
* AnnotationIndex
 * uima.tcas.Annotation
  * org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
   - org.apache.ctakes.typesystem.type.textsem.EntityMention

or

   * org.apache.ctakes.typesystem.type.textsem.EventMention
    - org.apache.ctakes.typesystem.type.textsem.EventMention.MedicationEventMention

Then select org.apache.ctakes.typesystem.type.textsem.EntityMention or
org.apache.ctakes.typesystem.type.textsem.EventMention.MedicationEventMention.
This will show an Annotation Index in the lower frame. Select any
annotation in that lower frame and you will see the text discovered in
the Text frame on the right.
You may close the CAS Visual Debugger (CVD) if you wish.