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From "Pei Chen (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-198) Drug NER only create drug signatures for RXNOM. Should it be extended to all identified MedicationEventMention?
Date Fri, 24 May 2013 19:29:21 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-198?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13666584#comment-13666584
] 

Pei Chen commented on CTAKES-198:
---------------------------------

+1,  I wonder if it is just legacy reasons why the coding scheme check was performed.  I.e.
before we had the MedicationEventMention subclass.  Perhaps others could chime in.
I think it would make sense to apply the drug signatures to any code that creates a MedicationEventMention.

--Pei
                
> Drug NER only create drug signatures for RXNOM. Should it be extended to all identified
MedicationEventMention?
> ---------------------------------------------------------------------------------------------------------------
>
>                 Key: CTAKES-198
>                 URL: https://issues.apache.org/jira/browse/CTAKES-198
>             Project: cTAKES
>          Issue Type: Improvement
>          Components: ctakes-drug-ner
>    Affects Versions: future enhancement
>            Reporter: Chen Lin
>            Priority: Minor
>              Labels: patch
>
> In DrugMentionAnnotator of the drug-ner module, it is hard-coded to only add drug signatures
(e.g. dosage, status change, strength, etc.) for RXNOM terms. Shouldn't the check for RXNOM
be removed, so that signatures can be added for all MedicationEventMentions?   
> while (uniqueNER.hasNext())
> 		{
> 			tokenAnt = (MedicationEventMention) uniqueNER.next();
> 			boolean isDrugNER = false;
> 			FSArray ocArr = tokenAnt.getOntologyConceptArr();
> 			if (ocArr != null)
> 			{
> 				for (int i = 0; i < ocArr.size() && !isDrugNER; i++)
> 				{
> 					OntologyConcept oc = (OntologyConcept) ocArr.get(i);
> 					String scheme = oc.getCodingScheme();
> 					if (scheme.compareTo("RXNORM") == 0)
> 					{
> 						isDrugNER = true;
> 					}
> 				}
> 			}

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