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From shady hussein <>
Subject Re: Combining Drug and Concept annotations
Date Mon, 04 Feb 2013 19:52:33 GMT
Hi Pei,
   Thanks for your reply, Yes i meant that DrugAggregatePlaintextUMLSProcessor return more
concepts, or the opposite AggregatePlaintextUMLSProcessor returns the usual concepts + the
MedicationEventMentions. I don't think it is hard to implement, as i think the dictionary
lookup code won't change.

I tried to merge the drug lookup in the lookupDB and add the drug annotator in the normal
pipe line, but of course things are not that simple :) I don't fully understand how the dictionary
look up works, otherwise i could do it. Maybe if you have sometime, you can guide me a little
and i can go from there.


On Feb 4, 2013, at 6:58 PM, "Chen, Pei" <> wrote:

> Hi Shady,
> Just wanted to confirm:
> Did  you mean that the DrugAggregatePlaintextUMLSProcessor identifies the same drugs,
but just with more attributes (i.e. dosage, frequency, etc.)?
> Or did you mean that the DrugAggregatePlaintextUMLSProcessor actually returned more UMLSConcepts
(MedicationEventMentions) the regular AggregatePlaintextUMLSProcessor?
> For the former, there is an outstanding Jira item to combine the 2 (reusing the existing
lookup entries- rather than a second lookup):
>> -----Original Message-----
>> From: Shady Hussein []
>> Sent: Monday, February 04, 2013 5:47 AM
>> To:
>> Subject: Combining Drug and Concept annotations
>> Dear All,
>>   I discovered that cTAKES doesn't recognize all the medical entities as
>> concepts. There is a difference between using the normal UMLS dictionary in
>> "/cdpdesc/analysis_engine/AggregatePlaintextUMLSProcessor.xml" and
>> "/drugnerdesc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml
>> ". The later can detect all the drugs, while the first can't.
>> My question now is how to combine between both of those dictionaries. So i
>> can detect all the drugs and concepts mentioned in the text. I would be
>> grateful if somebody can help me :)
>> --
>> Thanks and best Regards,
>> Shady AbdelAziz

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