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From Nick Nikandish <snika...@emerginghealthit.com>
Subject RE: OrangeBookFilterConsumerImpl
Date Wed, 25 Jun 2014 16:02:39 GMT
Hi Pei,

Thanks, I used NamedEntityLookupConsumerImpl that you mentioned now  that but I am getting
an error here: 

Map<String, org.apache.ctakes.typesystem.type.refsem.OntologyConcept> medicationAnnotator(JCas
aJCas){
    	Map<String, org.apache.ctakes.typesystem.type.refsem.OntologyConcept> ocMap = 
        		new HashMap<String, org.apache.ctakes.typesystem.type.refsem.OntologyConcept>();
        FSIndex medIndex = aJCas.getAnnotationIndex(MedicationMention.type); 
        Iterator<MedicationMention> medIter = medIndex.iterator();
        
        while (medIter.hasNext())
        {
        	MedicationMention medMen = medIter.next();  
        	ocMap.put(medMen.getCoveredText().toLowerCase(), medMen.getOntologyConceptArr(0));
    	} 
        System.out.println("Medication: "+ patternLists.createPatternList(ocMap.keySet()).toLowerCase());
        return ocMap;
        		
    }

I wrote this code in my own annotator to retrieve  the medication names but this is not returning
anything now. Which class should I  use now to get medication names?

-----Original Message-----
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu] 
Sent: Wednesday, June 25, 2014 11:53 AM
To: dev@ctakes.apache.org
Subject: RE: OrangeBookFilterConsumerImpl

Nick,
If I'm reading it correctly, that code change essentially tells it to bypass the OrangeBookFilter
completely.
If that is the behavior you're looking for (i.e. return all of the drugs bypassing the OrangeBookFilter,
then you can just modify the lookupConsumer className in your LookupDesc_Db.xml.  Try something
like the NamedEntityLookupConsumerImpl.class or similar (i.e. no filters) I don't recall the
exact name on the top of my head.
--Pei

From: Nick Nikandish [mailto:snikandi@emerginghealthit.com]
Sent: Wednesday, June 25, 2014 11:38 AM
To: dev@ctakes.apache.org
Subject: OrangeBookFilterConsumerImpl

Hi There,

I am using Ctakes and have added my own annotators that utilize CTakes. I need to use the
medication annotator so I can retrieve the medication names. In OrangeBookFilterConsumerImpl
class , consumeHits() method has a statements:
final boolean isValid = isValid( "trade_name", text ) || isValid( "ingredient", text );

It filters out some medication that I actually need. I made this change "boolean isValid=
ture"  to the code and made it work but I was wondering if there was another way like changing
something in the xml files that  have the same impact  without changing the code?


Thanks,
Nick Nikandish
Product Development Software Engineer
Clinical Research Informatics

Emerging Health
Montefiore Information Technology
6 Executive Blvd. Suite 290, Yonkers, NY 10701
914-457-6792 Office
snikandi@montefiore.org<mailto:snikandi@montefiore.org>
www.emerginghealthit.com<http://www.emerginghealthit.com/>
www.montefiore.org<http://www.montefiore.org/>

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