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From "Murphy, Sean P." <Murphy.S...@mayo.edu>
Subject RE: How to use Drug NER
Date Mon, 10 Mar 2014 16:36:33 GMT
Hey Ravi,
                I could be mistaken and if so, hopefully, someone else from the cTAKES community
can set me straight.  However, even if the dictionary resource is shipped it will not be available
until it is authorized via the DictionaryLookupAnnotatorDB.xml in the Drug NER pipeline. 
  There will be fields for your user name and password within this xml file that you can provide
your authentication credentials.
                Thanks,
                                ~Sean

From: ravi garg [mailto:ravigarg27@gmail.com]
Sent: Monday, March 10, 2014 11:21 AM
To: user@ctakes.apache.org
Subject: Re: How to use Drug NER

Hey Sean,
Thanx for the reply. I think what you are talking about is the clinical-pipeline but I want
to run Drug - NER pipeline. The external resources provided has a dictionary named rxnorm_index
which has around 162563 terms in it. So I guess it should be able to annotate that, but I
believe I am not using it correctly.
Regards,
Ravi

On Mon, Mar 10, 2014 at 9:44 PM, Murphy, Sean P. <Murphy.Sean@mayo.edu<mailto:Murphy.Sean@mayo.edu>>
wrote:
Good morning Ravi,

I believe only a sample dictionary is provided which uses a simple case where 'aspirin' would
be annotated.  The UMLS provided dictionary will need to be enabled to access the actual rxnorm_index.
 You will require a UMLS profile to access the dictionary resource provided. There should
be details on how to include the UMLS profile and password information in your environment.
 Let me know if you need further assistance.
                Thanks,
                                ~Sean

From: ravi garg [mailto:ravigarg27@gmail.com<mailto:ravigarg27@gmail.com>]
Sent: Monday, March 10, 2014 11:05 AM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: How to use Drug NER

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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