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From "Murphy, Sean P. [RO BIT]" <Murphy.S...@mayo.edu>
Subject RE: DrugAggregateUMLSPlainTextProcessor related question
Date Mon, 29 Apr 2013 14:04:11 GMT
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


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