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From ravi garg <ravigar...@gmail.com>
Subject Re: How to use Drug NER
Date Tue, 11 Mar 2014 07:37:47 GMT
Ohh Okay, I am sorry Sean, I didn't actually knew Rxnorm is an umls
dictionary and you need to have a license to use it. I have got that
working but still I dont get any annotations in drugner.type for example
RouteAnnotation, DurationAnnotation etc. Any ideas on how to get that
working

Thanks,
Ravi


On Mon, Mar 10, 2014 at 11:56 PM, ravi garg <ravigarg27@gmail.com> wrote:

> 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
>



-- 
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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