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Step | Example | |||||||||||||||||
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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:
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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.
Linux:
| Windows:
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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.
| Windows:
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5. Copy (or move) the resources to cTAKES_HOME.
| Windows:
Linux:
Mac OSX:
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Recommended) Add UMLS access rights
Note |
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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. |
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Step | Example | ||||||||||||
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1. Open a command prompt and change to the cTAKES_HOME directory.
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Linux:
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2. Start the CAS Visual Debugger by running this command: | Windows:
Linux:
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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. |
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4. An analysis engine (AE) needs to be loaded in order to process text.
rather than
Use the Run-> Load AE menu bar command. Navigate to the file
Click Open.
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5. From the menu bar, click Run -> Run AggregatePlaintextProcessor or "Run AggregatePlaintextUMLSProcessor".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:
This will show an AnnotationIndex in the lower frame. Select any annotation in that lower frame and you will see the text discovered in
Now select items in the lower frame to see the text being annotated. |
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