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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject Are you looping through all EntityMentions - read below about issue CTAKES-190
Date Wed, 17 Apr 2013 16:58:05 GMT
If you have written code that looks at all EntityMentions, please read cTAKES-190 (below) where
I describe why dictionary lookup will be changed to create some named entities as subtypes
of EventMention rather than EntityMention. And so something that previously looked at all
EntityMentions might now want to look at all IdentifiedAnnotations, since it is the superclass
of both EventMention and EntityMention.

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 offhand, please post details or add to the JIRA issue.  Thanks.

-- James


> -----Original Message-----
> From: notifications-return-517-Masanz.James=mayo.edu@ctakes.apache.org
> [mailto:notifications-return-517-Masanz.James=mayo.edu@ctakes.apache.org]
> On Behalf Of James Joseph Masanz (JIRA)
> Sent: Wednesday, April 17, 2013 11:41 AM
> To: ctakes-notifications@incubator.apache.org
> Subject: [jira] [Created] (CTAKES-190) dictionary lookup should create
> specific XxxxMention annotations instead of more generic EntityMention
> 
> James Joseph Masanz created CTAKES-190:
> ------------------------------------------
> 
>              Summary: 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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