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From ravi garg <ravigar...@gmail.com>
Subject Re: How to use Drug NER
Date Mon, 10 Mar 2014 18:26:33 GMT
Hey Xiayuan,

I ensured that the directory of the resource that is the rxnorm_index is
correct and cTAKES is also actually using it. I can see the logs wherein
cTAKES actually parses 16k docs. I get no errors though on using the
pipeline but nothing is extracted or annotated. Even the dosage, frequency
and route which I believe are not dependent on drug dictionary are also not
getting identified. I have worked on the main clinical pipeline before but
am working on the Drug pipeline for the first time so no idea whats wrong.

Regards,
Ravi


On Mon, Mar 10, 2014 at 11:38 PM, Xiayuan Huang <huangxy@cs.wisc.edu> wrote:

> Hi Ravi,
>
> Currently I am doing one project using cTAKES. I am trying to use a
> pipeline for identifying smoking status, SimulatedProdSmokingTAE.xml. And I
> also encountered some problem on executing those pipelines. Some possible
> errors will be the directory of UIMA resource, you have to set that
> correctly. And I got some exceptions when I try to run pipelines. We can
> discuss how to implement cTAKES later on, I guess I really need someone to
> discuss and help out on this cTAKES system.
>
> Best,
> Xiayuan Huang
>
>
>
> On 2014-03-10 11:05, ravi garg wrote:
>
>> Hey,
>>
>> I am using DrugAggregatePlainTextProcessor.xml as my analysis engine
>> annotator. I have downloaded all the required resources by cTAKES 3.1
>> . I guess it uses the rxnorm_index as the drug database. But I am not
>> getting any annotations as the output. Please let me know the correct
>> way using Drug NER
>>
>> Thanks,
>> Ravi
>>
>> --
>>
>> Ravi Garg
>> 4th Year
>> MSc (hons) Biological Sciences
>> B.E (hons) Computer Science and Engineering
>> BITS Pilani KK Birla Goa Campus
>>
>


-- 
Ravi Garg
4th Year
MSc (hons) Biological Sciences
B.E (hons) Computer Science and Engineering
BITS Pilani KK Birla Goa Campus

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