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Posted to user@ctakes.apache.org by Pieter Sheth-Voss <sh...@gmail.com> on 2013/03/12 20:45:52 UTC
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+Install+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.
Re: new user - why might cTAKES not recognize most of these concepts?
Posted by Pieter Sheth-Voss <sh...@gmail.com>.
Incredible. This system is simply amazing at identifying the clinical
terms in narrative descriptions.
RE: new user - why might cTAKES not recognize most of these
concepts?
Posted by "Masanz, James J." <Ma...@mayo.edu>.
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. <Ma...@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.
Re: new user - why might cTAKES not recognize most of these concepts?
Posted by Pieter Sheth-Voss <sh...@gmail.com>.
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. <Ma...@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.
RE: new user - why might cTAKES not recognize most of these
concepts?
Posted by "Masanz, James J." <Ma...@mayo.edu>.
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.