[jira] [Created] (CTAKES-190) dictionary lookup should create specific XxxxMention annotations instead of more generic EventMention

["James Joseph Masanz (JIRA)" <ji...@apache.org>]

James Joseph Masanz created CTAKES-190:
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             Summary: dictionary lookup should create specific XxxxMention annotations instead of more generic EventMention
                 Key: CTAKES-190
                 URL: https://issues.apache.org/jira/browse/CTAKES-190
             Project: cTAKES
          Issue Type: Bug
          Components: ctakes-dictionary-lookup
    Affects Versions: 3.1
            Reporter: James Joseph Masanz
            Assignee: James Joseph Masanz
             Fix For: 3.1


This is a follow-on to CTAKES-18 add XxxxEntity|EventMention types for other NEs similar to MedicationEventMention


There is a bug where dictionary lookup is annotating mentions of
sign/symptom, disease/disorder, and procedure as EntityMention rather
than EventMention, which does not follow the intent of the original
type system design.

Plus, with the changes to the type system in this two jira issues 
CTAKES-57	Type System updates for 3.x-incubating
CTAKES-18	add XxxxEntity|EventMention types for other NEs similar to MedicationEventMention
the dictionary lookup component needs to be updated to make use of the 
more specific XxxxMention types.

Within ctakes-dictionary-lookup, for named entities other than 
MedicationEventMention, the following two classes create annotations 
of EntityMention instead of the more specific types like 
AnatomicalSiteMention.

UmlsToSnomedConsumerImpl.java
NamedEntityLookupConsumerImpl.java

I'll be changing those two classes so that instead of creating 
EntityMention, the appropriate specific XxxxxxxMention type will 
be created.

Note this means that some will be created as subtypes of EventMention 
rather than subtypes of EntityMention, so something that previously looked
at all EntityMentions might now want to look at all IdentifiedAnnotations

The code that creates the annotaions within dictionary lookup will be this:

   if ( conceptKey == CONST.NE_TYPE_ID_DRUG ) {
       neAnnot = new MedicationEventMention( jcas );
   } else if ( conceptKey == CONST.NE_TYPE_ID_ANATOMICAL_SITE ) {
       neAnnot = new AnatomicalSiteMention( jcas );
   } else if ( conceptKey == CONST.NE_TYPE_ID_DISORDER ) {
       neAnnot = new DiseaseDisorderMention( jcas );
   } else if ( conceptKey == CONST.NE_TYPE_ID_FINDING ) {
       neAnnot = new SignSymptomMention( jcas );
   } else if ( conceptKey == CONST.NE_TYPE_ID_LAB ) {
       neAnnot = new LabMention( jcas );
   } else if ( conceptKey == CONST.NE_TYPE_ID_PROCEDURE ) {
       neAnnot = new ProcedureMention( jcas );
   } else {
       neAnnot = new EntityMention( jcas );
   }
   neAnnot.setTypeID( conceptKey );

I will be scanning the code for places that are looking at all 
EntityMentions and assuming it includes sign/symptom, disease/disorder,
and procedure annotations.

But if you are aware of such places and can save me some time,
please post details or add to the JIRA issue.



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