incubator-ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: Combining Drug and Concept annotations
Date Fri, 08 Feb 2013 02:42:49 GMT
In LookupDesc_Db.xml, trying changing this line
			<lookupConsumer className="edu.mayo.bmi.uima.lookup.ae.OrangeBookFilterConsumerImpl">
To this:
			<lookupConsumer className="edu.mayo.bmi.uima.lookup.ae.NamedEntityLookupConsumerImpl">

-- James

> -----Original Message-----
> From: ctakes-dev-return-1172-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1172-Masanz.James=mayo.edu@incubator.apache.org]
> On Behalf Of Masanz, James J.
> Sent: Thursday, February 07, 2013 1:33 PM
> To: 'ctakes-dev@incubator.apache.org'
> Subject: RE: Combining Drug and Concept annotations
> 
> 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[ct
> > > ak 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

Mime
View raw message