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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: what dictates full medication mention?
Date Thu, 02 Jan 2014 20:41:49 GMT
Using Luke to search the drug index, It (RxNorm code 328608) doesn't seem to be inside the
default rx_norm dictionary...

Don't recall the attributes that was used to build the index, but it could be due to the fact
that it was 'RXN_OBSOLEETED 07/31/2009'?

--Pei







> -----Original Message-----

> From: Masanz, James J. [mailto:Masanz.James@mayo.edu]

> Sent: Thursday, January 02, 2014 2:52 PM

> To: 'dev@ctakes.apache.org'

> Subject: RE: what dictates full medication mention?

>

> cTAKES annotates all mentions it finds, so if a shorter one is part of a longer

> one, you are supposed to get both/all, just as you are seeing with Ibuprofen

> and Ibuprofen 100MG.

>

> Offhand I don't know why the Drug NER cTAKES is not also creating a

> org.apache.ctakes.typesystem.type.textsem.MedicationMention for

> "Propranolol 40 MG".  It's not creating one for me either.  I'm using

> DrugAggregatePlaintextUMLSProcessor.xml

> And when I look at UMLS via the UTS, I see an rxnorm entry Propranolol 40

> MG [A10426756/RXNORM/SCDC/328608] for C1123553.

>

> Drug NER component uses a lucene index of terms from RxNorm. It's

> possible that term is missing from the index.  I can check on that later today

> or tomorrow if no one else beats me to it.

>

> I would do it using the Luke tool to inspect the lucene index in ctakes-

> resources-

> 3.1.0\resources\org\apache\ctakes\drugner\lookup\rxnorm_index

>

> -- James

>

>

> -----Original Message-----

> From: dev-return-2355-Masanz.James=mayo.edu@ctakes.apache.org

> [mailto:dev-return-2355-Masanz.James=mayo.edu@ctakes.apache.org] On

> Behalf Of Chase Master

> Sent: Thursday, January 02, 2014 1:30 PM

> To: dev@ctakes.apache.org

> Subject: what dictates full medication mention?

>

> Hi,

>

> I have a quick question.  When I run the cTAKES drugNER module on

> "Ibuprofen 100 MG" and "Propranolol 40 MG", I get an annotation for both

> Ibuprofen 100MG and Ibuprofen for the first case, but for the second case I

> only get Propranolol, by itself.  It does show the strength as 40MG for

> Propranolol, but it doesn't create a medication mention with full covered text

> as "Propranolol 40 MG".

> Both of these have the same semantic type, I noticed ( [T200]).

>

> Thanks,

> Chase

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