Versions Compared

Old Version 76

changes.mady.by.user Unknown User (bleeker)

Saved on

compared with

New Version 77

changes.mady.by.user Unknown User (james-masanz)

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: clarify test1.xml uses AggregateCdaProcessor.xml - jira CTAKES-42

...

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-3.0.0-incubating

Linux:

Code Block
languagenone
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:

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 and the CAS Consumer , which contains a CDA file(s).
Within the CAS Consumers pane of the same window, change the 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 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.

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 an aggregate 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

...