[CTAKES-357] Adding support for mention of Medical Devices

• Type: Improvement
• Status: Open
• Priority: Minor
• Resolution: Unresolved
• Affects Version/s: 3.2.1, 3.2.2
• Fix Version/s: future enhancement
• Component/s: ctakes-type-system
• Assignee: Unassigned
• Reporter: Bruce Tietjen
• Created: 04/May/15 15:04
• Updated: 06/Mar/17 16:47

Description

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 ); }