I tried it but it doesn't give me the required results. Now it annotates the drugs as "Concept" and "MedicationEventMention" but there are still some drugs which are not annotated while it is annotated as "MedicationEventMention" if i used "DrugAggregatePlaintextUMLSProcessor.xml". You can try this scenario with this text
DISCHARGE MEDICATIONS : 1. Tegretol 200 mg p.o. t.i.d. 2. Klonopin 1 mg p.o. b.i.d. 3. Colace 100 mg p.o. b.i.d. 4. Nicoderm 21 mg q d. topical . 5. Zofran 24 mg p.o. q d. x 3 days . Here "Colace" and "Nicoderm" are not annotated but are annotated as "MedicationEventMention" when you use "DrugAggregatePlaintextUMLSProcessor.xml". Thanks for your help and looking forward to your reply On Wed, Feb 6, 2013 at 3:14 AM, Masanz, James J. <[email protected]>wrote: > > I'm attaching something you can try. > > I'm assuming you are using cTAKES 2.5. > 1) put the attached file in cTAKESdesc\cdpdesc\analysis_engine > 2) update > cTAKESdesc\lookupdesc\analysis_engine\DictionaryLookupAnnotatorUMLS.xml > with your UMLS username and password > 3) update the other copy of DictionaryLookupAnnotatorUMLS.xml in > cTAKESdesc\drugnerdesc\analysis_engine also with your UMLS username and > password > > -- James Masanz > ________________________________________ > From: > ctakes-dev-return-1136-Masanz.James=mayo....@incubator.apache.org[ctakes-dev-return-1136-Masanz.James= > [email protected]] on behalf of shady hussein [ > [email protected]] > Sent: Monday, February 04, 2013 1:52 PM > To: [email protected] > Subject: Re: Combining Drug and Concept annotations > > 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. > > Thanks, > Shady > > On Feb 4, 2013, at 6:58 PM, "Chen, Pei" <[email protected]> > 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): > https://issues.apache.org/jira/browse/CTAKES-20 > > > >> -----Original Message----- > >> From: Shady Hussein [mailto:[email protected]] > >> Sent: Monday, February 04, 2013 5:47 AM > >> To: [email protected] > >> 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 > -- Thanks and best Regards, Shady AbdelAziz
