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Step

Example

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

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cd \cTAKES-3.0

Linux:

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cd /usr/bin/cTAKES-3.0


Note
titleNote

cTAKES_HOME must be your current directory unless you are skilled at setting paths on your machine.

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

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bin\runctakesCVD.bat

Linux:

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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

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

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

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

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 4. Copy the example text in the example at the right (from the next cell ) in this table 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: 

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<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) application if you wish. 
  
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