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From Pei Chen <chen...@apache.org>
Subject Re: ctakes not capturing all meds/rxnorm IDs
Date Mon, 22 Sep 2014 13:40:55 GMT
James,
If you could share some examples, I'll take a closer look.
But in the meantime, in your LookupDesc_Db.xml [1], I believe you can
just use the NamedEntityLookupConsumerImpl instead of the
UmlsToSnomedDbConsumerImpl.
While you're there, you may also consider expanding the Lookup Window
or Parts Of Speech exclusions...

[1] http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml

On Mon, Sep 22, 2014 at 2:17 AM, EM Gladiators <emgladiators@gmail.com> wrote:
> Pei,  I am not seeing anything being filtered in the logs.  I checked both
> the output in the terminal and also I set the log in the software to log
> everything.  How do I go about suppressing the OrangeBook filter and use
> only Rxnorm?  I'm still not sure the filtering is the problem, because
> aspirin is also found in OrangeBook.  But, removing the OrgangeBook filter
> would be a good place to start to see if it improves the medication name
> recognition.
>
> Thank you,
>
> James
>
> On Sun, Sep 21, 2014 at 10:30 PM, Pei Chen <chenpei@apache.org> wrote:
>>
>> In the logs, do you see something like "Filtered out xyz"?
>> I think the default configuration has a OrangeBook Filter consumer
>> applied.  That is only RxNorm concepts that also exist in the
>> OrangeBook are returned.  I'm not sure if this is causing some of your
>> drugs to be missed, but worth taking out OrangeBook filter out to
>> confirm.
>> We should probably default all RxNorm to be returned and make the
>> OrangeBook filter optional in the future release.
>>
>> On Sun, Sep 21, 2014 at 5:53 PM, EM Gladiators <emgladiators@gmail.com>
>> wrote:
>> > I have recently installed ctakes.  I am using the
>> > AggregatePlaintextUMLSProcessor.  When running the CVD, it is not
>> > accurately
>> > annotating all medication names.  Specific medication names that it
>> > annotates correctly are metformin and nifedipine.  Specific medications
>> > it
>> > fails to annotate are aspirin and simvastatin.  It is unclear why some
>> > names
>> > would be annotated correctly and some not, even though all medication
>> > names
>> > are found in rxnorm.  I am afraid that it is not correctly using the
>> > rxnorm
>> > files.  Is there a way to check to see if the full rxnorm is being
>> > searched?
>> >
>> > I have not had a problem with snomed CT terms, ctakes does appear to be
>> > capturing these correctly.
>> >
>> > Thank you,
>> >
>> > James Foster
>> >
>> > My setup is as follows...
>> >
>> > Mac OS 10.9.4
>> > Java version 1.8.0_20
>> > ctakes version 3.2.0 with optional resources package
>
>

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