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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 19:53:52 GMT

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+Developer+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+Instal
> 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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