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To use them, you must have a UMLS username and password, and an Internet connection.

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Step

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Example

3. UMLS user ID and password.

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If you plan to use the UMLS Resources, set/export env variables \\
export ctakes.umlsuser=\[username\], ctakes.umlspw=\[password\] \\
or add the system properties to the java args \\
\-Dctakes.umlsuser=<username> \-Dctakes.umlspw=<password> 

In order to integrate the dictionaries you will need to do two things:
(1) Change the UMLSUser and UMLSPW <nameValuePair> strings in these descriptor files with your UMLS username and password.

• Dictionary Lookup: <cTAKES_HOME>/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
• (optional) Drug NER: <cTAKES_HOME>/desc/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml

The following shows where in the files you would make the changes. (Do not change the <configurationParameters> by the same name.)

      <nameValuePair>
        <name>ctakes.umlsuser</name>
        <value>
          <string>YOUR_UMLS_USERNAME_HERE</string>
        </value>
      </nameValuePair>
      <nameValuePair>
        <name>ctakes.umlspw</name>
        <value>
          <string>YOUR_UMLS_PASSWORD_HERE</string>
        </value>
      </nameValuePair>

(2) Include the DictionaryLookupAnnotatorUMLS.xml Analysis Engine within your aggregate Analysis Engine or switch to the ones provided by cTAKES. cTAKES has provided duplicates of shipped Analysis Engine descriptors, put UMLS in the name, and placed DictionaryLookupAnnotatorUMLS.xml within them for these components:

• Dictionary Lookup
• Clinical Documents pipeline
• Drug NER
• Side Effect

So you simply need to switch to using those descriptors. For example, if you were using AggregateCdaProcessor.xml in the Clinical Documents pipeline you would switch to using AggregateCdaUMLSProcessor.xml instead and you will now hook into the complete dictionaries.

You can, of course, modify your own aggregate Analysis Engine files and place the DictionaryLookupAnnotatorUMLS.xml Analysis Engine within them.
Since this is an in-memory database implementation, please be patient during the initial load as it could take approximately 20-30 seconds for the database to initialize.

Building Your Own Dictionaries

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