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Date: Mon, 6 Mar 2017 16:47:32 +0000 (UTC)
From: "James Joseph Masanz (JIRA)" <jira@apache.org>
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Subject: [jira] [Updated] (CTAKES-357) Adding support for mention of Medical
 Devices
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archived-at: Mon, 06 Mar 2017 16:47:37 -0000


     [ https://issues.apache.org/jira/browse/CTAKES-357?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

James Joseph Masanz updated CTAKES-357:
---------------------------------------
    Affects Version/s: 3.2.2
           Issue Type: Improvement  (was: Bug)

> Adding support for mention of Medical Devices
> ---------------------------------------------
>
>                 Key: CTAKES-357
>                 URL: https://issues.apache.org/jira/browse/CTAKES-357
>             Project: cTAKES
>          Issue Type: Improvement
>          Components: ctakes-type-system
>    Affects Versions: 3.2.1, 3.2.2
>            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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