Versions Compared

Old Version 30

changes.mady.by.user Unknown User (bleeker)

Saved on

compared with

New Version 31

changes.mady.by.user Unknown User (bleeker)

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Step

Example

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

Code Block
languagenone
cd \apache-ctakes-3.0.0-incubating\bin

Linux:

Code Block
languagenone
cd /usr/local/apache-ctakes-3.0.0-incubating/bin


Note
titleNote

cTAKES_HOME 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:

Code Block
languagenone
bin\runctakesCVD.bat

Linux:

Code Block
languagenone
bin/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:

Code Block
languagenone
<cTAKES_HOME>/testdata/cdptest/testinput/plaintext/testpatient_plaintext_1.txt


Warning

This file may not be in the binary distribution only src?


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.
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:

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:
Windows:

Code Block
languagenone
cd \apache-ctakes-3.0.0-incubating\bin

Linux:

Code Block
languagenone
cd /usr/local/apache-ctakes-3.0.0-incubating/bin


Note
titleNote

Note that cTAKES<cTAKES_HOME 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:

Code Block
languagenone
bin\runctakesCPE.bat

Linux:

Code Block
languagenone
bin/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

37

4. Navigate to the file

Code Block
languagenone
<cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml

Click Open.

No example  

5. Click the Play button (green/blue play arrow near the bottom).

  38

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:

Code Block
languagenone
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:

Code Block
languagenone
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:

Code Block
languagenone
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:

Code Block
languagenone
c:\stuff\diff-html.html

Linux:

Code Block
languagenone
/tmp/diff-html.html

 

...