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Step

Example

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

Note

Note that <cTAKES_HOME>/bin must be your current directory unless you are skilled at setting paths on your machine.


Windows:

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cd \apache-ctakes-3.0.0-incubating\bin

Linux:

note
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cd /usr/local/apache-ctakes-3.0.0-incubating/bin

Note that <cTAKES_HOME>/bin 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: The application may take a minute to start on slower hardware. 
 Windows:
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runctakesCVD.bat

Linux:
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runctakesCVD.sh

The application may take a minute to start on slower hardware. 
 No example 
 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. 
 This example file can also be found in test data
 Info
If you have been directed here as a developer the path to a copy of this file is here: 
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<cTAKES_HOME>/ctakes-clinical-pipeline/src/
test/data
testdata/plaintext/testpatient_plaintext_1.txt



 Warning
This file may not be in the binary distribution only srcused to be in a binary distribution as well: 
 <cTAKES_HOME>/desc/ctakes-clinical-pipeline/src/testdata/plaintext/testpatient_plaintext_1.txt 
 Is it only in src now? Does it not exist?

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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. 
 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


Note: A development environment will not have the first "desc/" in the path. 
 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: 
 Wiki Markup
CAS Index Repository \\
\* SofaIndex \[0\] \\
\* AnnotationIndex \[1\] \\  
 
 5. From the menu bar, click Run -> Run AggregatePlaintextProcessor. 
 
 6. You'll get a list of all the annotations for this clinical document in the Analysis Results frame. Annotations such as concepts mentioned, 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.medfacts.types.Concept 
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 problem 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.MedicationEventMention
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. 
 
...
 Step 
 Example 
 1. Open a command prompt and change to the cTAKES_HOME directory: cTAKES_HOME directory: 
 Note
Note that <cTAKES_HOME>/bin must be your current directory unless you are skilled at setting paths on your machine.

 Windows:
 Code Block
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cd \apache-ctakes-3.0.0-incubating\bin

Linux:
note
 Code Block
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cd /usr/local/apache-ctakes-3.0.0-incubating/bin

Note that <cTAKES_HOME>/bin must be your current directory unless you are skilled at setting paths on your machine.
 2. Start the collection processing engine by running this command: 
 Windows:
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runctakesCPE.bat

Linux:
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runctakesCPE.sh

The application may take a minute to start on slower hardware. 
 No example 
 3. This will bring up the Collection Processing Engine Configurator. In the Menu bar click File >Open CPE Descriptor 
  
 4. Navigate to the file
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<cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml

Click Open. 
 Info
If you have been directed here as a developer the first "desc/" will not be in the path.
 No example 
 5. Click the Play button (green/blue play arrow near the bottom). 
  
 6. You should see that one document was processed. You did process a collection of documents. In this case the collection only contained one just to show how to do it. Close the results window. 

 7. Close the CPE application. You may be prompted to save changes. Since this was just a test you may click the No button. 
 
 8. Open a new command prompt and change to the <cTAKES_HOME> 
 
 9. To test the results there is a comparison tool that will help show that the results match expectations with the following syntax:
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java -cp ctakes-utils-3.0.0.jar org.apache.ctakes.utils.xcas_comparison.Compare
<First File> <Second File> <diff-html>

Where: <First File> is the first file to compare; <Second File> is the second file to compare; <diff-html> is where the results are written to 
 Copy and paste the example at the right (next cell) which has had our 
 example files already substituted into a command prompt to run. In this 
 case we have shipped an example of what the output should be for you to 
 compare against. 
 Windows: 

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java -cp ctakes-utils-3.0.0.jar org.apache.ctakes.utils.xcas_comparison.Compare ^
"testdata\cdptest\testoutput\plaintext\sample_note_plaintext.xml" ^
"testdata\cdptest\testsampleoutput\plaintext\sample_note_plaintext.xml" ^
c:\stuff\diff-html.html


 Linux:
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java -cp ctakes-utils-3.0.0.jar org.apache.ctakes.utils.xcas_comparison.Compare \
"/usr/bin/cTAKES3.0/testdata/cdptest/testoutput/plaintext\sample_note_plaintext.xml" \
"/usr/bin/cTAKES3.0/testdata/cdptest/testsampleoutput/plaintext/sample_note_plaintext.xml" \
/tmp/diff-html.html

 10. The resulting file will open for you. Look at the comparison to see the annotations resulting from this pipeline. 
 Windows:
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c:\stuff\diff-html.html

Linux:
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/tmp/diff-html.html

 
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