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Comment: Migrated to Confluence 5.3
Section
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width65%
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titleContents of this Page
Table of Contents
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Include Page
CTAKES:Menu cTAKES 3.1 to IncludeCTAKES:
Menu cTAKES 3.1 to Include

...

Step

Example

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

Note

It is best if <cTAKES_HOME> is your current directory. The scripts will change directories, so being home to run the command is best.


Windows:

Code Block
languagenone
cd \apache-ctakes-3.1.0

Linux:

Code Block
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cd /usr/local/apache-ctakes-3.1.0

2. Start the CAS Visual Debugger by running this command:
The application may take a minute to start on slower hardware.

Windows:

Code Block
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bin\runctakesCVD.bat

Linux:

Code Block
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bin/runctakesCVD.sh

3. Copy the example text from the next cell in this table and paste the contents into the Text section of CVD, replacing the text that is already there.

You can also download a copy of the file from here

Code Block
langnone
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.

4. An analysis engine (AE) needs to be loaded in order to process text.
If you installed the optional UMLS resources, use

No Format
AggregatePlaintextUMLSProcessor.xml

rather than

No Format
AggregatePlaintextProcessor.xml

in this step.
Use the Run-> Load AE menu bar command. Navigate to the file

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

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

unmigrated-wiki-markup


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


5. From the menu bar, click Run -> Run AggregatePlaintextProcessor or "Run AggregatePlaintextUMLSProcessor".


6. You'll get a list of all the annotations for this clinical document in the Analysis Results frame. Annotations such as named entities, division by sentence, etc from the pipeline are viewable. To see one, in the Analysis Results frame, click on the key in front of:

CAS Index Repository
* AnnotationIndex
 * uima.tcas.Annotation
  * org.apache.ctakes.typsystem.type.textsem.IdentifiedAnnotation
   * org.apache.ctakes.typsystem.type.textsem.EventMention

This will show an AnnotationIndex 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 like the concept of the disease/disorder Hyperlipidemia.

For a medication example select this

CAS Index Repository
* AnnotationIndex
 * uima.tcas.Annotation
  * org.apache.ctakes.typsystem.type.textsem.IdentifiedAnnotation
   * org.apache.ctakes.typsystem.type.textsem.EventMention
    * org.apache.ctakes.typsystem.type.textsem.MedicationMention

Now select items in the lower frame to see the text being annotated.

You may close the CAS Visual Debugger (CVD) application if you wish.


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