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From "Steven Bethard (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-190) dictionary lookup should create specific XxxxMention annotations instead of more generic EntityMention
Date Wed, 26 Jun 2013 20:06:21 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-190?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13694209#comment-13694209
] 

Steven Bethard commented on CTAKES-190:
---------------------------------------

> I scanned the code for places that were looking at all EntityMentions and assuming it
includes sign/symptom, disease/disorder, and 
> procedure annotations, and made updates where needed to look at IdentifiedAnnotations
and then check if EntityMention or 
> EventMention, r1479635.

Some of the remaining issues are that both DegreeOfRelationExtractorAnnotator and EntityMentionPairRelationExtractorAnnotator
are still selecting EntityMentions in code like:

List<EntityMention> args = JCasUtil.selectCovered(...)

I'm working on these issues now, but the models will also need to be retrained once I've fixed
the code.
                
> dictionary lookup should create specific XxxxMention annotations instead of more generic
EntityMention
> ------------------------------------------------------------------------------------------------------
>
>                 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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