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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.

Prerequisites

 

 

Step

 

 

Example

1. Make sure you have Java 1.8 or higher.

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 "1.8.0_201" Java(TM) SE Runtime Environment ...


Linux:

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user@system:/$ java -version
java version "1.8.0_201"
OpenJDK Runtime Environment ...

Install cTAKES

 

...

Step

 

 

Example

1. On the cTAKES downloads page, download the User Installation package.

Info

The download time will be commensurate with ~650 MB of data.

 

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

From the following directory, download the signature file that corresponds to your download from step 1

https://www.apache.org/dist/ctakes/ctakes-4.0.0/ 

Please do not download any of the files that end with .zip or .gz directly from apache.org/dist - use the downloads page listed in step 1 if you need to download cTAKES itself so that a mirror can be used.

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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>. It is the directory that contains subdirectories like bin, desc, resources, lib.

You will need to refer to this directory later.

Windows:

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C:\apache-ctakes-4.0.0

Linux:

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/usr/local/apache-ctakes-4.0.0

Windows:

Linux:

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tar -xvf apache-ctakes-4.0.0.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-4.0-bin.zip
 
sudo unzip ctakes-resources-4.0-bin.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-4.0-bin\resources C:\apache-ctakes-4.0.0\resources

Linux:

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cp -R /tmp/resources/* /usr/local/apache-ctakes-4.0.0/resources

Mac OSX:

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ditto /tmp/resources/* /usr/local/apache-ctakes-4.0.0/resources
6. If you created your own dictionaries for use with a previous release of cTAKES and you plan to use them with cTAKES 4.0, you must convert your dictionaries to be compatible with cTAKES 4.0, which is described in the next section. The dictionaries installed by the above steps do not need to be converted. 

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CAS Visual Debugger (CVD)

 

...

Step

 

 

Example

1. Open a command prompt and change to the cTAKES_HOME directory, which is the directory that contains subdirectories like bin, desc, resources, lib.

Depending on how you extracted the files,

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-4.0.0
  -- or --
cd \apache-ctakes-4.0.0-bin\apache-ctakes-4.0.0\

Linux:

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cd /usr/local/apache-ctakes-4.0.0
  -- or --
cd /usr/local/apache-ctakes-4.0.0-bin/apache-ctakes-4.0.0

2. This step uses AggregatePlaintextFastUMLSProcessor, which requires that you downloaded the cTAKES resources as described in step 4 of Install cTAKES (above) and that you added UMLS access rights (also above).

If you haven't done those, you can use the AggregatePlaintextProcessor instead.

Start the CAS Visual Debugger and load the AggregatePlaintextFastUMLSProcessor pipeline by running this command (at right)


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

The GUI opens and then loads the AggregatePlaintextFastUMLSProcessor pipeline. If it appears to be hung, look at the window where you entered the command and you will see what is happening.

Once the analysis engine has successfully loaded you should see a tree in the Analysis Results frame:

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

 

Windows:

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bin\runctakesCVD.bat  desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml

Linux:

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bin/runctakesCVD.sh  desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml

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. From the menu bar, click Run -> Run AggregatePlaintextFastUMLSProcessor.

Note: If you would like to TEST some simple annotators to ensure it's working without UMLS, you can just load:

/desc/ctakes-core/desc/analysis_egine/SentencesAndTokensAggregate.xml

 

5. 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. 

 

To run other pipelines, use the Run-> Load AE menu bar command.

Navigate to the file you wish to load, such as

 

<cTAKES_HOME>
  /desc
    /ctakes-clinical-pipeline
      /desc
        /analysis_engine
          /AggregatePlaintextProcessor.xml

 

Click Open. 
Loading the analysis engine may take a minute. The lower right corner of the window shows the name of the currently-loaded pipeline if a pipeline was loaded successfully.

                                                    


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

 

Collection Processing Engine (CPE)

 

...

Step

 

 

Example

1. Open a command prompt and change to the cTAKES_HOME directory, which is the directory that contains subdirectories like bin, desc, resources, lib.

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-4.0.0

Linux:

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cd /usr/local/apache-ctakes-4.0.0

2. Create a directory for some test data.

mkdir testdata

3. The sample dictionary that does not require UMLS rights contains only a few terms.

Create a file containing the sentence at right into the testdata directory.

The patient says they took 325 mg aspirin for knee pain.

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 following file, which uses the AggregatePlaintextProcessor

 

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


Click Open.

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7. Change the Collection Reader input directory to testdata, which contains the files to process

Within the CAS Consumers pane of the same window, change the output directory to testdata/output

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

Info

What just happened? The pipeline used a file system reader that will process all files in a directory. The processing was accomplished by a pipeline of cTAKES components. For each input file, one resultant file was placed into the output directory. Each output file is an XML file that includes the annotations made by each component within the pipeline. (The AggregatePlaintextProcessor allows for the Chunk Creator Class parameter to be passed to the Chunker annotator.)

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 Performance Report window.

Note

This example of using the CPE GUI did not use the UMLS resources. If you wish to perform named entity recognition or concept identification for anything other than a few words, you will need to 1) obtain the rights to use UMLS resources 2) add those credentials to cTAKES, and 3) use a pipeline that makes use of those UMLS resources (see above).

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

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