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From "Bruce Tietjen (JIRA)" <j...@apache.org>
Subject [jira] [Created] (CTAKES-357) Adding support for mention of Medical Devices
Date Mon, 04 May 2015 15:05:06 GMT
Bruce Tietjen created CTAKES-357:
------------------------------------

             Summary: Adding support for mention of Medical Devices
                 Key: CTAKES-357
                 URL: https://issues.apache.org/jira/browse/CTAKES-357
             Project: cTAKES
          Issue Type: Bug
          Components: ctakes-type-system
    Affects Versions: 3.2.1
            Reporter: Bruce Tietjen
            Priority: Minor
             Fix For: future enhancement


To add support for annotating Medical Devices:

Adding a DeviceMention that uses EntityMention as the supertype:

TypeSystem.xml:
    <typeDescription>
   <name>org.apache.ctakes.typesystem.type.textsem.DeviceMention</name>
      <description>Corresponds to the UMLS Devices semantic group: medical device and
research device.</description>
      <supertypeName>org.apache.ctakes.typesystem.type.textsem.EntityMention</supertypeName>
      <features>
       <featureDescription>
          <name>entity</name>
          <description/>
          <rangeTypeName>org.apache.ctakes.typesystem.type.refsem.Entity</rangeTypeName>
        </featureDescription>
      </features>
    </typeDescription>


Changes to UmlsToSnomedConsumerImpl.java:
  - add a configuration parameter for deviceTuis (along side the existing medicationTuis,
procedureTuis, etc.)
        static private final String DEVICE_TUIS_PRP_KEY = "deviceTuis";
        private Set<String> _deviceTuiSet = new HashSet<>();
  - load the list in the constructor (UmlsToSnomedConsumerImpl) and add it to _validTuiSet:
      _deviceTuiSet = loadList( props.getProperty( DEVICE_TUIS_PRP_KEY ) );    // 8
      _validTuiSet.addAll( _deviceTuiSet );

  - add code to getNamedEntityType to set their type to CONST.NE_TYPE_ID_DEVICE
          } else if ( _deviceTuiSet.contains( tui ) ) {
             return CONST.NE_TYPE_ID_DEVICE;
         }


  - in consumeHits, add:
                 } else if ( conceptKey == CONST.NE_TYPE_ID_DEVICE ) {
                      neAnnot = new DeviceMention( jcas );
                 }





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