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From "ASF subversion and git services (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-190) dictionary lookup should create specific XxxxMention annotations instead of more generic EntityMention
Date Thu, 27 Jun 2013 20:15:20 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-190?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13695022#comment-13695022
] 

ASF subversion and git services commented on CTAKES-190:
--------------------------------------------------------

Commit 1497555 from [~steven.bethard]
[ https://svn.apache.org/r1497555 ]

CTAKES-190 - Fixes most of relation-extractor issues. All code now uses SHARPKnowtatorXMLReader
to ensure that all annotations are loaded with their correct type system types. Relation extractor
classes produce DegreeOfTextRelation and LocationOfTextRelation objects. The modifier extractor
has also been updated to work with the new types, but is not yet able to produce things like
BodyLateralityModifier - instead it just produces generic Modifiers with their typeID set
appropriately.
                
> 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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