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Posted to notifications@ctakes.apache.org by "ASF subversion and git services (JIRA)" <ji...@apache.org> on 2013/07/01 19:26:22 UTC
[jira] [Commented] (CTAKES-190) dictionary lookup should create
specific XxxxMention annotations instead of more generic EntityMention
[ https://issues.apache.org/jira/browse/CTAKES-190?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13696984#comment-13696984 ]
ASF subversion and git services commented on CTAKES-190:
--------------------------------------------------------
Commit 1498579 from james-masanz@apache.org
[ https://svn.apache.org/r1498579 ]
CTAKES-190 - comment that MedicationMention should be used instead of MedicationEventMention as of 3.1. (Will make several separate commits because of timeouts occurring while svn is temporarily routed through EU)
> 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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