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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: new user - why might cTAKES not recognize most of these concepts?
Date Tue, 12 Mar 2013 20:10:31 GMT

Yes, the section I pointed you at is in the developer instructions.
We'll need to get some of that copied over to the user instructions so people don't have to
go to developer instructions in order to use their UMLS user ID and password.

I created JIRA item CTAKES-176 so this doesn't get forgotten.
https://issues.apache.org/jira/browse/CTAKES-176

-- James

> -----Original Message-----
> From: ctakes-user-return-76-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-user-return-76-Masanz.James=mayo.edu@incubator.apache.org]
> On Behalf Of Pieter Sheth-Voss
> Sent: Tuesday, March 12, 2013 3:02 PM
> To: ctakes-user@incubator.apache.org
> Subject: Re: new user - why might cTAKES not recognize most of these
> concepts?
> 
> Brilliant, thanks you so much!
> 
> I see it now under Developer setup.     I hadn't peeked  ahead to
> Developer, figuring I was just a user at this stage.
> 
> Pieter
> 
> On Tue, Mar 12, 2013 at 3:53 PM, Masanz, James J. <Masanz.James@mayo.edu>
> wrote:
> >
> > Hi Peiter,
> >
> > The dictionary used in that example only contains a handful of terms.
> > To use a more complete dictionary, you need a UMLS user ID and password.
> >
> > It looks like we could improve our documentation to make that more
> obvious. Thanks.
> >
> > For now, please see the step " UMLS user ID and password." on this page:
> > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Develope
> > r+Install+Guide
> >
> >
> > Regards,
> > James Masanz
> >
> >> -----Original Message-----
> >> From:
> >> ctakes-user-return-74-Masanz.James=mayo.edu@incubator.apache.org
> >> [mailto:ctakes-user-return-74-Masanz.James=mayo.edu@incubator.apache.
> >> org]
> >> On Behalf Of Pieter Sheth-Voss
> >> Sent: Tuesday, March 12, 2013 2:46 PM
> >> To: ctakes-user@incubator.apache.org
> >> Subject: new user - why might cTAKES not recognize most of these
> concepts?
> >>
> >> Learning the cTAKES user application.  Successfully downloaded,
> >> installed and loaded the application and the separate vocabulary.
> >> Copied the following example from the intro tutorial
> >> (https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+User+I
> >> nstal
> >> l+Guide)
> >> and added a number of extra medical terms as a test.
> >>
> >> It successfully parses using [Run->Run AggregatePlainTextProcessor].
> >> But strangely it recognizes only a very few medical terms as Concepts
> >> in [AnnotationIndex - > uima.tcas.Annotation ->
> >> org.apache.ctakes.assertion.medfacts.types.Concept]
> >>
> >> 1.   "Hyperlipidemia"
> >> 2.  "Aspirin"
> >> 3. "Knee"
> >> 4.  "Pain"
> >>
> >> It doesn't recognize "BMI", "Asthma", "Hypertension", "lupus",
> >> "inflammatory arthritis", "TNF inhibitor", doxycycline, etc.
> >>
> >> Why might that be?
> >> Thanks!
> >>
> >> Pieter Sheth-Voss, PhD
> >>
> >> ==========================================================
> >> Dr. Nutritious
> >>
> >> Medical Nutrition Therapy for Hyperlipidemia, Hypertension, Asthma
> >> and lupus.
> >> Referral from: Julie Tester, RD, LD, CNSD Phone contact: (555)
> >> 555-1212
> >> Height: 144 cm Current Weight: 45 kg Date of current weight:
> >> 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
> >> Diet: General
> >> Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for
> >> activity.
> >> Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
> >> Pt has been on a 3-day calorie count and has had an average intake of
> >> 1100 calories.
> >> She was instructed to drink 2-3 cans of liquid supplement to help
> >> promote weight gain.
> >> She agrees with the plan and has my number for further assessment.
> >> May want a Resting Metabolic Rate as well. She takes an aspirin a day
> >> for knee pain, asthma, rheumatoid arthritis, headache, dizziness, and
> >> hyperlipidemia.
> >>   Patient currently taking aspirin, acetaminophen, hydrocodone,
> >> orencia, rituximab, and placebo.
> >>
> >> A 35 y/o male with HLA B27-positive inflammatory arthritis with
> >> severe acne, currently on Indocin and Arava, where the acne is not
> >> responding to TNF inhibitor drugs, and has previously failed
> >> isotretinoin and doxycycline.
> >>
> >> Patient has asthma, currently taking albuterol and a leukotriene-
> >> inhibitor.

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