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Comment: added -desc to the bin/runctakesCVD.sh example command

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Step

Example

1. Open a command prompt and change to the cTAKES_HOME directory, which is the directory that contains subdirectories like bin, desc, resources, lib.

Depending on how you extracted the files,

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-4.0.0
  -- or --
cd \apache-ctakes-4.0.0-bin\apache-ctakes-4.0.0\

Linux:

Code Block
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cd /usr/local/apache-ctakes-4.0.0
  -- or --
cd /usr/local/apache-ctakes-4.0.0-bin/apache-ctakes-4.0.0

2. This step uses AggregatePlaintextFastUMLSProcessor, which requires that you downloaded the cTAKES resources as described in step 4 of Install cTAKES (above) and that you added UMLS access rights (also above).

If you haven't done those, you can use the AggregatePlaintextProcessor instead.

Start the CAS Visual Debugger and load the AggregatePlaintextFastUMLSProcessor pipeline by running this command (at right)


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

The GUI opens and then loads the AggregatePlaintextFastUMLSProcessor pipeline. If it appears to be hung, look at the window where you entered the command and you will see what is happening.

Once the analysis engine has successfully loaded you should see a tree in the Analysis Results frame:

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

 

Windows:

Code Block
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bin\runctakesCVD.bat  desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml

Linux:

Code Block
languagenone
bin/runctakesCVD.sh  -desc  desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml

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. From the menu bar, click Run -> Run AggregatePlaintextFastUMLSProcessor.

Note: If you would like to TEST some simple annotators to ensure it's working without UMLS, you can just load:

/desc/ctakes-core/desc/analysis_egine/SentencesAndTokensAggregate.xml

 

5. 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. 

 

To run other pipelines, use the Run-> Load AE menu bar command.

Navigate to the file you wish to load, such as

 

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

 

Click Open. 
Loading the analysis engine may take a minute. The lower right corner of the window shows the name of the currently-loaded pipeline if a pipeline was loaded successfully.

                                                    


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

 

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