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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: Combining Drug and Concept annotations
Date Thu, 07 Feb 2013 19:32:33 GMT
The clinical documents pipeline (cdpdesc/analysis_engine/AggregatePlaintextUMLSProcessor.xml)
filters the drug mentions it finds, using the Orange Book.
The drug NER pipeline does not do that filtering.
I suspect that accounts for the differences you are seeing.
The pipeline logs a message when it filters out a drug due to not finding it in the version
of the Orange Book that is included within cTAKES.

If you need pointers on how to remove that filtering, I can take a look at that later today.

-- James

> -----Original Message-----
> From: ctakes-dev-return-1156-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1156-Masanz.James=mayo.edu@incubator.apache.org]
> On Behalf Of Shady Hussein
> Sent: Wednesday, February 06, 2013 4:21 AM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: Combining Drug and Concept annotations
> 
> 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.
> <Masanz.James@mayo.edu>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.xm
> > l
> > 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.edu@incubator.apache.org[ctak
> > es-dev-return-1136-Masanz.James= mayo.edu@incubator.apache.org] on
> > behalf of shady hussein [ shady.aziz@gmail.com]
> > Sent: Monday, February 04, 2013 1:52 PM
> > To: ctakes-dev@incubator.apache.org
> > 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"
> > <Pei.Chen@childrens.harvard.edu>
> > 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:shady.aziz@gmail.com]
> > >> Sent: Monday, February 04, 2013 5:47 AM
> > >> To: ctakes-dev@incubator.apache.org
> > >> 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.x
> > >> ml ". 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

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