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title	Contents of this Page

Table of Contents

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Include Page

	CTAKES:Menu cTAKES 3.1 to IncludeCTAKES:
	Menu cTAKES 3.1 to Include

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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:
Use wget to obtain the *.TAR.GZ file.
wget <URL of the file from downloads>

Info
The download time will be commensurate with ~165MB of data.

Windows:

Linux:

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HTTP request sent, awaiting response... 200 OK
Length: 763500777 (728M) [application/x-gzip]
Saving to: `apache-ctakes-3.1.0-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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C:\apache-ctakes-3.1.0

Linux:

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/usr/local/apache-ctakes-3.1.0

Windows:

Linux:

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tar -xvf apache-ctakes-3.1.0-bin.tar.gz -C /usr/local

4. Download the cTAKES resources ZIP file with a matching version from the ctakesresources project (More information on cTAKES models). These resources are required to operate cTAKES.

Info
Due to licensing considerations resources are hosted at an external location. For ease of installation, a single package was created with all the resources you will need. Licensing for these resources is found within the download.

Info
Download time will be commensurate with 1GB of data.

Unzip the cTAKES resources file into a temporary location.

Windows:

Linux:

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cd /tmp
wget http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip
sudo unzip ctakes-resources-3.1.0.zip

5. Copy (or move) the resources to cTAKES_HOME.
Copy the contents of the temporary resources directory (and all sub-directories) to <cTAKES_HOME>/resources.

Info
There may be conflicts while taking this action. Overwrite the cTAKES_HOME files with those in the resources download.

Windows:

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xcopy /s C:\temp\ctakes-resources-3.1.0\resources C:\apache-ctakes-3.1.0\resources

Linux:

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cp -R /tmp/resources/* /usr/local/apache-ctakes-3.1.0/resources

Mac OSX:

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ditto /tmp/resources/* /usr/local/apache-ctakes-3.1.0/resources

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(Optional) Add UMLS access rights

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Step

Example

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

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:

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cd \apache-ctakes-3.1.0

Linux:

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cd /usr/local/apache-ctakes-3.1.0

2. Start the CAS Visual Debugger by running this command:
The application may take a minute to start on slower hardware.

Windows:

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bin\runctakesCVD.bat

Linux:

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bin/runctakesCVD.sh

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

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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.
If you installed the optional UMLS resources, use

No Format
AggregatePlaintextUMLSProcessor.xml

rather than

No Format
AggregatePlaintextProcessor.xml

in this step.
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:

unmigrated-wiki-markup

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

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

6. 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.

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

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(Optional) Add UMLS access rights