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Step

Example

1. Navigate to the cTAKES downloads page on the Apache site and download the binary package. Select a mirror site and press the Change button to modify the URL to your desired mirror location before doing the download or accept the default.

Windows:
Download the ZIP file.
Linux:
Take the link for the file you want and use wget to obtain the *.TAR.GZ file.
wget <URL of the file>

Windows:

Linux:

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Resolving people.apache.org... 140.211.11.9
Connecting to people.apache.org|140.211.11.9|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 763500777 (728M) [application/x-gzip]
Saving to: `apache-ctakes-3.0.0-incubating-bin.tar.gz'

13% [===========>                                     ] 106,548,331 1.13M/s eta 11m 9s

2. (Optional but recommended) Verify the downloaded files against a file signature to ensure you have the proper and complete file.

No example

3. Unzip the file you downloaded into a directory that you want to be the cTAKES install location. The compressed files contain a single directory at the top level. This folder we will call <cTAKES_HOME>. You will need to refer to this directory later.

Windows:

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cC:\apache-ctakes-3.0.0-incubating

Linux:

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/usr/local/apache-ctakes-3.0.0-incubating

This folder we will call <cTAKES_HOME>. You will need to refer to this directory later.

Windows:

Linux:

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tar -xvf apache-ctakes-3.0.0-incubating-bin.tar.gz -C /usr/local

4. Download UMLS and model resources...

Warning

The location of these resources is not prepared yet. Replace this box with instructions.

No example

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Step

Example

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

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cd \cTAKESapache-ctakes-3.0.0-incubating

Linux:

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cd /cTAKES/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.

 

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

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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 \[1\] \\

 

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:

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

MAY NOT BE IN THE BINARY DISTRIBUTION ONLY SRC?

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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.

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

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.typesystem.type.textsem.EventMention.MedicationEventMention


Then select org.apache.ctakes.typesystem.type.textsem.EntityMention or
org.apache.ctakes.typesystem.type.textsem.EventMention.MedicationEventMention.
This will show an Annotation Index 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.
You may close the CAS Visual Debugger (CVD) application if you wish.

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Step

Example

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

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cd C:\cTAKES3\apache-ctakes-3.0.0-incubating

Linux:

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cd /usr/bin/cTAKES3local/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:

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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

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.

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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