Sean, Thanks for taking the time.
Best Regards Kannan On Mon, Apr 29, 2013 at 3:11 PM, Murphy, Sean P. [RO BIT] < [email protected]> 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:* [email protected] [mailto: > [email protected]] *On Behalf Of *Kannan > Thiagarajan > *Sent:* Monday, April 29, 2013 3:00 PM > *To:* [email protected] > *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] < > [email protected]> 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:* [email protected] [mailto: > [email protected]] *On Behalf Of *Kannan > Thiagarajan > *Sent:* Monday, April 29, 2013 7:52 AM > *To:* [email protected] > *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
