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From Pieter Sheth-Voss <shethv...@gmail.com>
Subject Re: new user - why might cTAKES not recognize most of these concepts?
Date Tue, 12 Mar 2013 20:02:07 GMT
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+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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