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These instructions are under construction.

These instructions are for end users. With these instructions you can install cTAKES, configure it, and use it to process text (typically text associated with a medical record). If you were planning to expand, change, or modify the code within cTAKES, refer to the cTAKES 3.0 Developer Guide.

These instructions will cover installation and a test of the main product including trained models for sentence detection and tagging parts of speech, dictionaries from a subset of the UMLS, a very small subset of the full LVG resource, etc. Optional components are described in the Component Use Guide.

Once you have finished installing cTAKES, you will be able to see what cTAKES is capable of. Further exploitation of the software's ability may require following a few additional steps involving what dictionaries are being used. The last section on this page covers these next steps.

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:

java -version

Windows:

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:

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)

Install cTAKES

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>

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

Windows:
Apache cTAKES > cTAKES 3.0 User Install Guide > snap031.png
Linux:

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:

C:\apache-ctakes-3.0.0-incubating

Linux:

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

Windows:
Apache cTAKES > cTAKES 3.0 User Install Guide > snap033.png
Linux:

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

4. Download cTAKES 3.0 Dictionaries and models.

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.

Go to http://sourceforge.net/projects/ctakesresources/files/ and download the ZIP file with a matching version from the ctakesresources project.
Download time will be commensurate with 1GB of data.
Unzip the files into a temporary location.

Windows:

C:\temp\ctakes-resources-3.0.1\resources

Linux:

/tmp/ctakes-resources-3.0.1/resources

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.

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

Windows:

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

Linux:

cp /tmp/ctakes-resources-3.0.1/resources/* /usr/local/apache-ctakes-3.0.0-incubating/resources/*

Process documents using cTAKES

This version allows you to test most components bundled in cTAKES in two different ways:

Using the bundled UIMA CAS Visual Debugger (CVD) to view the results stored as XCAS files or run the annotators
Using the bundled UIMA Collection Processing Engine (CPE) to process documents in cTAKES_HOME/testdata directory

You will need a windowing environment on Linux to run these tools.

CAS Visual Debugger (CVD)

Step

Example

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

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:

cd \apache-ctakes-3.0.0-incubating

Linux:

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:

bin\runctakesCVD.bat

Linux:

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.

If you have been directed here as a developer the path to a copy of this file is here:

<cTAKES_HOME>/ctakes-clinical-pipeline/src/testdata/plaintext/testpatient_plaintext_1.txt

You can also download a copy of the file from

https://svn.apache.org/repos/asf/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-clinical-pipeline/src/test/data/plaintext/testpatient_plaintext_1.txt

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

<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:

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

Apache cTAKES > cTAKES 3.0 User Install Guide > snap034.png

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

Apache cTAKES > cTAKES 3.0 User Install Guide > snap035.png

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.

Apache cTAKES > cTAKES 3.0 User Install Guide > snap036.png

Collection Processing Engine (CPE)

Step

Example

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

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:

cd \apache-ctakes-3.0.0-incubating

Linux:

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

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

Windows:

bin\runctakesCPE.bat

Linux:

bin/runctakesCPE.sh

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

Apache cTAKES > cTAKES 3.0 User Install Guide > snap037.png

4. Navigate to the file

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

Click Open.

If you have been directed here as a developer the first "desc/" will not be in the path.

No example

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

Apache cTAKES > cTAKES 3.0 User Install Guide > snap038.png

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:

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:

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:

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:

c:\stuff\diff-html.html

Linux:

/tmp/diff-html.html

Using the same CVD and CPE programs in the manner described above, you can test all the other components. The analysis engines and collection processing engines shipped with cTAKES for some of the annotators are described in the following table.

Annotator	Description	Abbreviated	Example Analysis Engine (AE)	Example Collection processing Engine (CPE)	Example test data
Clinical Document Pipeline	the complete cTAKES pipeline to obtain majority of cTAKES annotations	cdp	cTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml	cTAKES_HOME/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml	cTAKES_HOME/testdata/cdptest
Chunker	obtain cTAKES chunking annotations	chunker	cTAKES_HOME/desc/ctakes-chunker/desc/ChunkerAggregate.xml	cTAKES_HOME/desc/ctakes-chunker/desc/ChunkerCPE.xml	cTAKES_HOME/testdata/chunkertest
Dependency Parser	obtain dependency parsing tree	dp	cTAKES_HOME/desc/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedInfPosAggregate.xml	cTAKES_HOME/desc/ctakes-dependency-parser/desc/collection_processing_engine/ClearParserTestCPE.xml	cTAKES_HOME/testdata/dptest
Drug NER	the annotator to obtain drug annotations	drugner	cTAKES_HOME/desc/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcesor.xml	cTAKES_HOME/desc/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml	cTAKES_HOME/testdata/drugnertest
Dictionary Lookup	mapping cTAKES annotations to dictionaries (e.g., SNOMED_CT or RxNorm	lookup	cTAKES_HOME/desc/ctakes-dictionary-lookup/desc/analysis_engine/TestAggregateTAE.xml	cTAKES_HOME/desc/ctakes-dictionary-lookup/desc/collection_processing_engine/LookupCPE.xml	cTAKES_HOME/testdata/lookuptest
PAD Term Spotter	identifying terms related to PAD	pad	cTAKES_HOME/desc/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml	cTAKES_HOME/desc/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_Sample.xml	cTAKES_HOME/testdata/padtest
Smoking Status	the annotator to obtain document or patient-level smoking status	smoking	cTAKES_HOME/desc/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml	cTAKES_HOME/desc/ctakes-smoking-status/desc/collection_processing_engine/Sample_SmokingStatus_output_flatfile.xml	cTAKES_HOME/testdata/smokingtest
Side Effect	the annotator to find side effect mentions and sentences from clinical documents	sideeffect	cTAKES_HOME/desc/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE.xml	cTAKES_HOME/desc/ctakes-side-effect/desc/collection_processing_engine/SideEffectCPE.xml	cTAKES_HOME/testdata/sideeffecttest

Next Steps

The cTAKES 3.0 Component Use Guide will help you to understand, in great detail, each of the cTAKES components that have been installed. In some cases you can learn how to improve the components.

Also, before you go on to process text in production you will need to consider dictionaries and models. cTAKES does not distribute from Apache a complete dictionary capable of annotating production data. The models provided have been trained on data that may not match your data well enough to be effective. In most cases, you will need to modify the dictionaries and train models on your own data to be effective.