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From Kannan Thiagarajan <kanna...@gmail.com>
Subject Re: DrugAggregateUMLSPlainTextProcessor related question
Date Tue, 30 Apr 2013 00:04:43 GMT
Sean,

Thanks for taking the time.

Best Regards
Kannan


On Mon, Apr 29, 2013 at 3:11 PM, Murphy, Sean P. [RO BIT] <
Murphy.Sean@mayo.edu> wrote:

>  cTAKES\resources\drugnerresources\lookup\LookupDesc_DrugNER.xml or
> similar has the setting under the lookup bindings maxPermutationLevel (as
> it states here that value used is ‘3’:****
>
> ** **
>
> <lookupInitializer className=*
> "edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl"*>****
>
>
> <properties>****
>
>
> <property key=*"textMetaFields"* value=*
> "preferred_designation|other_designation"*/>****
>
>
> <property key=*"maxPermutationLevel" *value=*"3"*/>****
>
>
> <property key=*"windowAnnotations"* value=*
> "edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation"*/>****
>
>
> <property key=*"exclusionTags"* value=*
> "CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB"*/> <!--
> ohnlp ID# 3378705 -->****
>
>
> </properties>****
>
>                                                 </lookupInitializer>****
>
> ** **
>
> *From:* user-return-175-Murphy.Sean=mayo.edu@ctakes.apache.org [mailto:
> user-return-175-Murphy.Sean=mayo.edu@ctakes.apache.org] *On Behalf Of *Kannan
> Thiagarajan
> *Sent:* Monday, April 29, 2013 3:00 PM
> *To:* user@ctakes.apache.org
> *Subject:* Re: DrugAggregateUMLSPlainTextProcessor related question****
>
> ** **
>
> Hello Sean,****
>
> ** **
>
> Thanks for the response. ****
>
> ** **
>
> Just for my own understanding, do you know how many permutations its
> currently limited to and where I might see that in the code****
>
> ** **
>
> Best Regards****
>
> Kannan****
>
> On Mon, Apr 29, 2013 at 9:04 AM, Murphy, Sean P. [RO BIT] <
> Murphy.Sean@mayo.edu> wrote:****
>
> Hello Kannan,****
>
>                 The issue is mainly due to how cTAKES is handling
> permutations.    The overhead required to handle, say 7 or more
> permutations, was not found to have a good return even if there was a
> corresponding RXCONSO entry.****
>
>                 Additionally, unless the text extracted represented the
> normalized form, according to Rxnorm, the resulting named entity would be
> missed.****
>
>  ****
>
>                 So for the example below, if Lexapro had a corresponding
> entry for ‘Lexapro 10 MG’ than the pipeline would have discovered the
> entity.****
>
>                 Thanks,****
>
>                                 ~Sean****
>
>                 ****
>
>  ****
>
> *From:* user-return-173-Murphy.Sean=mayo.edu@ctakes.apache.org [mailto:
> user-return-173-Murphy.Sean=mayo.edu@ctakes.apache.org] *On Behalf Of *Kannan
> Thiagarajan
> *Sent:* Monday, April 29, 2013 7:52 AM
> *To:* user@ctakes.apache.org
> *Subject:* DrugAggregateUMLSPlainTextProcessor related question****
>
>  ****
>
> Hello, ****
>
>  ****
>
> I'm trying to understand the named entity recognition aspect of cTAKES.***
> *
>
>  ****
>
> If I pass-in a text such as below****
>
>  ****
>
> *Lexapro 10 mg oral tablet 3 times a day*****
>
>  ****
>
> cTAKES finds a single MedicationEventMention with the RxNorm code =
> 352741.  However looking in the RXCONSO database, I see that there is one
> specific entry for the 10 mg. ****
>
>  ****
>
> 352741|ENG||||||1551887|1551887|352741||RXNORM|BN|352741|Lexapro||N|4096|*
> ***
>
> 352272|ENG||||||1937400|1937400|352272||RXNORM|SY|352272|Lexapro 10 MG
> Oral Tablet||N|4096|****
>
>  ****
>
> But, cTAKES always resorts to finding the first entry (without 10 mg). ***
> *
>
>  ****
>
> I did however notice that in certain cases it finds two annotations. For
> example****
>
>  ****
>
> *Aspirin 325 mg two times a day*
> ****
>
>  ****
>
> Comes up with two annotations - Asprin 325 mg (code 317300) and Aspirin
> (code 1191)****
>
>  ****
>
> 317300|ENG||||||1481682|1481682|317300||RXNORM|SCDC|317300|Aspirin 325
> MG||N|4096|****
>
> 1191|ENG||||||2596464|2596464|1191||MTHSPL|SU|R16CO5Y76E|Aspirin||N|4096|*
> ***
>
>  ****
>
> Any thoughts as to why there might be a difference in the lookup. ****
>
>  ****
>
>  ****
>
> Thanks****
>
>  ****
>
> --
> Best Regards****
>
> Kannan Thiagarajan****
>
>  ****
>
>
>
> ****
>
> ** **
>
> --
> Best Regards****
>
> Kannan Thiagarajan****
>
> ** **
>



-- 
Best Regards
Kannan Thiagarajan

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