Versions Compared

Old Version 7

changes.mady.by.user James Masanz

Saved on

compared with

New Version 8

changes.mady.by.user James Masanz

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Step

Example

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

No example

2. Once you have your UMLS username and password, edit the following files. Find the line lines in each script that runs java and add the ctakes.umlsuser and ctakes.umlspw parameters to the java command with your credentials. Make sure you substitute your actual ID and password if you cut and paste the example.

Windows:

Code Block
languagenone
<cTAKES_HOME>\bin\runctakesCVD.bat
<cTAKES_HOME>\bin\runctakesCPE.bat

Linux:

Code Block
languagenone
<cTAKES_HOME>/bin/runctakesCVD.sh
<cTAKES_HOME>/bin/runctakesCPE.sh
Code Block
languagenone
java -Dctakes.umlsuser=<YOUR_UMLS_ID_HERE> -Dctakes.umlspw=<YOUR_UMLS_PASSSWORD_HERE> -cp ...

If you use special characters in your user name or password, you may need to escape them or for windows, place the string in quotes

For example, if your username and password were literally myusername and mypassword, you could insert them before the -cp option so the start of the java command would look like this:

 

Code Block
java  -Dctakes.umlsuser=myusername  -Dctakes.umlspw=mypassword  -cp ...

Windows:

 If you use special characters in your umls user name or password, you can place them in double-quotes:

Code Block
java  -Dctakes.umlsuser="myuser!!!!"  -Dctakes.umlspw="mypass!!!!"  -cp ...

 

Linux:

 If you use special characters in your user name or password, you may need to escape them

...

  1. Using the bundled UIMA CAS Visual Debugger (CVD) to view the results stored as XCAS files or run the annotators
  2. Using the bundled UIMA Collection Processing Engine (CPE) to process documents in cTAKES_HOME/testdata directory
  3. Using the cTAKES 4.0 GUI

These tools On Linux, you will need a windowing environment to run these tools.

...

TBD

 

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:

Code Block
languagenone
cd \apache-ctakes-4.0.0

Linux:

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

Linux:

Code Block
languagenone
cd /usr/local/apache-ctakes-4.0.0
  -- or --
cd /usr/
Code Block
languagenone
cd /usr/local/apache-ctakes-4.0.0-bin/apache-ctakes-4.0.0

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


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.

Windows:

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

Linux:

Code Block
languagenonenone
bin/runctakesCVD.sh  desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xmlbin/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

Code Block
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.

4. An analysis engine (AE) needs to be loaded in order to process text.
If you installed the UMLS resources, use

No Format
AggregatePlaintextFastUMLSProcessor.xml


in this step.

Use the Run-> Load AE menu bar command. Navigate to the file

Code Block
languagenone
<cTAKES_HOME>
  /desc
    /ctakes-clinical-pipeline
      /desc
        /analysis_engine
          /AggregatePlaintextFastUMLSProcessor.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]

5. 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

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.

...

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:

Code Block
languagenone
cd \apache-ctakes-4.0.0

Linux:

Code Block
languagenone
cd /usr/local/apache-ctakes-4.0.0

2. Create a directory for some test data.

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:

Code Block
languagenone
bin\runctakesCPE.bat

Linux:

Code Block
languagenone
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 AggregateCdaProcessor

Code Block
langnone
<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, which contains a CDA file(s).

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? You placed a sample CDA document into the input of a pipeline. 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. The AggregateCdaProcessor allows for a parameter (Chunk Creator Class) to be passed to the Chunker annotator. 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.

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.

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.

No example

 

cTAKES GUI and Piper Files

TBD - TODO fill in this section on how to start the GUI and use Piper Files

The cTAKES GUI can be launched using the bin\runctakesGUI.bat or bin\runctakesGUI.sh file.

 

The analysis engines and collection processing engines shipped with cTAKES for some of the annotators are described in the following table.

...