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Once you have finished installing cTAKES and its separately-bundled resources, you will be able to see what cTAKES is capable of.

Note
If you wish to perform named entity recognition / concept identification for anything other than a few sample concepts, you will need to perform the optional step of installing the separately-bundled UMLS resources - see step 4. And you will need to use an aggregate that makes use of those UMLS resources.

Prerequisites

Step

Example

1. Make sure you have Java 1.6 or higher. Most systems come with Java already installed.

Run this command to check your version.

Windows and Linux:

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java -version

Windows:

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C:\>java -version
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
Java HotSpot(TM) Client VM (build 16.3-b01, mixed mode, sharing)

Linux:

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tbleeker@system:/$ java -version
java version "1.6.0_22"
OpenJDK Runtime Environment (IcedTea6 1.10.1) (6b22-1.10.1-0ubuntu1)
OpenJDK 64-Bit Server VM (build 20.0-b11, mixed mode)

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

Linux:

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

Windows:

Linux:

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

Optional steps - install UMLS resources and set UMLS password

Windows:

4. Download cTAKES 3.0 Dictionaries and models. These resources are required to operate cTAKES.

Info
Due to licensing considerations and easy of installability, one download from an external location was established 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.

Windows:
Go to cTAKES resources and download the ZIP file with a matching version from the ctakesresources project.
Unzip the files into a temporary location such as C:\temp.

Linux:
Obtain the URL of the version matching ZIP file from cTAKES resources, get the file, and unzip to a temporary location.

Windows:
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Linux:

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cd /tmp
wget http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.0.1.zip
sudo unzip ctakes-resources-3.0.1.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-3.0.1\resources C:\apache-ctakes-3.0.0-incubating\resources

Step

Example

4. Obtain a UMLS license if you don't already have one. You can request one at https://uts.nlm.nih.gov/license.html

No example

5. Edit the following files, adding in your UMLS user ID and password as parameters to the java command:

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bin\runctakesCVD.bat
bin\runctakesCPE.bat

Linux:

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bin/runctakesCVD.sh
bin/runctakesCPE.sh

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java -Dctakes.umlsuser=YOUR_ID_HERE -Dctakes.umlspw=YOUR_PASSSWORD_HERE -cp ...

6. Download cTAKES 3.0 Dictionaries and models. These resources are required to operate cTAKES.

Info
Due to licensing considerations and easy of installability, one download from an external location was established 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.

Windows:
Go to cTAKES resources and download the ZIP file with a matching version from the ctakesresources project.
Unzip the files into a temporary location such as C:\temp.
Linux:
Obtain the URL of the version matching ZIP file from cTAKES resources, get the file, and unzip to a temporary location. Windows:

Image Removed

Linux:

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cdcp -R /tmp
wget http:/resources/sourceforge.net/projects/ctakesresources/files/ctakes-resources* /usr/local/apache-ctakes-3.0.1.zip
sudo unzip ctakes-resources-3.0.1.zip

7. 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.

0-incubating/resources

(Optional) Add UMLS access rights

Note

In the initial setup cTAKES will recognize only few sample concepts in text. If you wish to perform named entity recognition or concept identification for anything other than these few words, you will need to 1) obtain the rights to use UMLS resources 2) add those credentials to cTAKES, and 3) use an aggregate that makes use of those UMLS resources. If you don't, cTAKES will work but won't recognize much.

Step

Example

1. If you do not have a UMLS username and password, you may request one at UMLS Terminology Services.

No example

2. Edit the following files, adding in your UMLS user ID and password as parameters to the java command:

Windows:

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bin\runctakesCVD.bat
bin\runctakesCPE.bat

Linux:

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bin/runctakesCVD.sh
bin/runctakesCPE.sh

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java -Dctakes.umlsuser=<YOUR_UMLS_ID_HERE> -Dctakes.umlspw=<YOUR_UMLS_PASSSWORD_HERE> -cp ...

Windows:

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xcopy /s C:\temp\ctakes-resources-3.0.1\resources C:\apache-ctakes-3.0.0-incubating\resources

Linux:

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cp -R /tmp/resources/* /usr/local/apache-ctakes-3.0.0-incubating/resources

Process documents using cTAKES

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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-3.0.0-incubating

Linux:

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

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

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AggregatePlaintextUMLSProcessor.xml

rather than than

none

No Format
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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:

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 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:

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-3.0.0-incubating

Linux:

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

2. Create a directory for some test data.

Windows:mkdir testdata

3. Download this sample file and place it into the testdata directory.

No example

4. Start the collection processing engine by running this command:
The application may take a minute to start on slower hardware.

Windows:

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bin\runctakesCPE.bat

Linux:

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bin/runctakesCPE.sh

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

6. Navigate to the file

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<cTAKES_HOME>
  /desc
    /ctakes-clinical-pipeline
      /desc
        /collection_processing_engine
          /test1.xml

Click Open.

No example

7. Change the Collection reader input directory to testdata and the CAS Consumer output directory to testdata/output in the CPE fields

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

Info

What just happened? You placed a sample CDA document into the input of a pipeline. The pipeline was a file system reader that will process all files in a directory. The processing was accomplished by the chunker cTAKES component (noted by the descriptor that you openedthe name of the Analysis Engine pictured). One resulting file for each input file was placed into the output directory. This output file is an XML file that annotates the noun phrases and verb phrases.

9. 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

10.

Note
This example of using the CPE GUI did not use the separately-downloaded UMLS resources. If you wish to perform named entity recognition

/

or concept identification for anything other than a few

sample concepts

words, you will need to

perform the optional step of installing the separately-bundled UMLS resources, and

1) obtain the rights to use UMLS resources 2) add those credentials to cTAKES, and 3) use an aggregate that makes use of those UMLS resources (see above).

Image Added No example

11 10. Close the CPE application. You may be prompted to save changes. Since this was just a test you may click the No button.

No example

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Versions Compared

Old Version 72

New Version 73

Key

Prerequisites

Optional steps - install UMLS resources and set UMLS password

(Optional) Add UMLS access rights

Process documents using cTAKES