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4. 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:

Step

Example

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

Code Block
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cd \apache-ctakes-3.0.0-incubating

Linux:

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


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.

No example 

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
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
Code Block
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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. 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 \[1\] \\

 

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<cTAKES_HOME>/testdata/cdptest/testinput/plaintext/testpatient_plaintext_1.txt

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.

3. From the menu bar, click Run -> Run AggregatePlaintextProcessor.
You'll get a list of all the annotations in the Analysis Results frame.

Image Removed 

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 \[1\] \\

Image Added

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

Image Added

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 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.typesystemtypsystem.type.textsem.EventMention.MedicationEventMention

Then select

IdentifiedAnnotation

   * org.apache.ctakes.

typesystem

typsystem.type.textsem.

EntityMention or

EventMention
    * org.apache.ctakes.

typesystem

typsystem.type.textsem

.EventMention

.MedicationEventMention

Now select items .
This will show an Annotation Index in the lower frame . Select any
annotation in that lower frame and you will to see the text discovered in
the Text frame on the rightbeing annotated.

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

Image Added Image Removed

Collection processing engine (CPE)

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

Linux:

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


Note
titleNote

Note that cTAKES_HOME 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
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bin\runctakesCPE.bat

Linux:

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bin/runctakesCPE.sh

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

 

3. This will bring up the Collection Processing Engine Configurator. In the Menu bar click File >Open CPE Descriptor Image Removed


4. Navigate to the file

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

Click Open.

 

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. Image Removed


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

 

...

  • Training a sentence detector model
  • Training a Part of Speech (POS) tagger model (Building a model Obtaining training data)
  • Creating a Part of Speech (POS) tag dictionary (Building a tag dictionary)
  • Training a chunker model (Building a model - Prepare GENIA training data)
  • Training a dependency parser (Dependency Parser)