ctakes-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: concept identification query
Date Fri, 12 Apr 2013 17:00:55 GMT
+1, and  I suggest it not just be mentioned, but that it be strongly mentioned. Maybe even
change some headings on that User Guide page to indicate the "Install" is of the code, not
of the real dictionaries.



Perhaps the heading  "Install cTAKES" could be changed to "Install cTAKES without UMLS dictionaries"



Or add a new section between these two

Install cTAKES

Process documents using cTAKES



Something like this

Install cTAKES

Install UMLS dictionaries (optional, but required to test Concept Identification on your own
data)

Process documents using cTAKES



And under  Process documents using cTAKES" we could have a big NOTE that says something like
"Be aware that if you have not installed the UMLS dictionaries, you only have a tiny sample
dictionary...."



Troy, you have done such a good job at the docs, I'll leave these are suggestions for you,
but I'd be happy to take a pass at drafting something on the Wiki if you'd prefer.



Regards,

James Masanz



From: user-return-113-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-113-Masanz.James=mayo.edu@ctakes.apache.org]
On Behalf Of giri vara prasad nambari

Sent: Friday, April 12, 2013 11:34 AM

To: user

Subject: Re: concept identification query



I second Tim's comment. Information in the link provided by Troy is really helpful, if "user
guide" has this link may be in ctakes-resources downloaded section, that helps users.



Right now I am limited myself as user of ctakes and trying to understand what I may get our
of the box, how much I need to customize to develop my idea into a to prototype.



You guys have been really helpful with quick replies with solution pointers. Few days back,
I was about to give-up, but with the help and pointers I am getting from you guys, motivated
me to stay with ctakes and explore more. Now I am almost ready to finalize infrastructure
and take-off for prototype development(few more things to hash-out and hoping they will be
quick).



Thanks again for your time and help.



Thank you,

Giri

On Fri, Apr 12, 2013 at 12:19 PM, Tim Miller <timothy.miller@childrens.harvard.edu>
wrote:

Troy,

My vote would be to mention in the user guide that "real" entity recognition requires the
umls component, and maybe a link to the developers guide where that is explained? Probably
there are some people who wouldn't know what to expect out of the box and will be disappointed
that it doesn't find much. (Luckily some of them email our lists and we can help them figure
it out, but there may be people who just figure it doesn't work very well and give up.)



Btw, the guides are really nice, great job on that.

Tim



On 04/12/2013 12:12 PM, Bleeker, Troy C. wrote:

The Developer install guide talks about UMLS integration: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide

Search for UMLS. It is described for Eclipse and for command line. Users that are just trying
out cTAKES don't have those instructions. Do you think they should be part of the User Guide?



Troy

From: user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org [mailto:user-return-110-Bleeker.Troy=mayo.edu@ctakes.apache.org]
On Behalf Of giri vara prasad nambari

Sent: Friday, April 12, 2013 11:06 AM

To: user@ctakes.apache.org

Subject: RE: concept identification query



Hi All,

Where do we need to update this UMLS key in ctakes?

Thanks for your time and help.

Thank you,

Giri

On Apr 12, 2013 10:59 AM, "Savova, Guergana" <Guergana.Savova@childrens.harvard.edu>
wrote:

You would need to get a UMLS license to get the full functionality. It takes 2-3 days to be
approved for it.

Hope this helps.

--Guergana



From: Rooney, Niall [mailto:nf.rooney@ulster.ac.uk]

Sent: Friday, April 12, 2013 10:26 AM

To: user@ctakes.apache.org

Subject: RE: concept identification query



Pei,



I don't have a UMLS license yet but thanks for looking into this.



From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]

Sent: 12 April 2013 15:10

To: <user@ctakes.apache.org>

Subject: Re: concept identification query



Thanks Tim for confirming...

AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.



Sent from my iPhone



On Apr 12, 2013, at 9:25 AM, "Tim Miller" <timothy.miller@childrens.harvard.edu> wrote:

Niall,

I'm sure Pei will get back to you soon, but just wanted to let you know, many of those entities
will be found by the standard ctakes installation. I get aphasia and stomach.  It does not
get blood pressure, I think because this is filtered out by UMLS semantic class - I think
it is categorized as a "measurement," and cTAKES will find things like disease/disorder, signs/symptoms,
and a few others, which this does not fit into exactly.  It may be worth thinking about how
to include it if it will be useful. In this example it looks like it's linked to some assessment
"HB +20%", I assume that is some measurement that would be useful to extract?

Tim

On 04/12/2013 07:05 AM, Rooney, Niall wrote:

Hi,



I have question concerning concept identification.  I have modifying the example text given
in the installation instructions to demonstrate the use of CAS Visual Debugger.



My text is:



Dr. Nutritious



Medical Nutrition Therapy for Hyperlipidemia and Aphasia



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 and blood pressure.

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 Metabolic Rate
as well. She takes Codeine a day for knee and stomach pain.





Original entities and concepts are identified such as "Hyperlidemia" , "knee","pain". However
concepts associated with addition to the text are not identified such as "Aphasia", "blood
pressure", "stomach".  Also "metabolic rate" is not identified. Does anyone know why this
is?







________________________________________



This email and any attachments are confidential and intended solely for the use of the addressee
and may contain information which is covered by legal, professional or other privilege. If
you have received this email in error please notify the system manager at postmaster@ulster.ac.uk
and delete this email immediately. Any views or opinions expressed are solely those of the
author and do not necessarily represent those of the University of Ulster. The University's
computer systems may be monitored and communications carried out on them may be recorded to
secure the effective operation of the system and for other lawful purposes. The University
of Ulster does not guarantee that this email or any attachments are free from viruses or 100%
secure. Unless expressly stated in the body of a separate attachment, the text of email is
not intended to form a binding contract. Correspondence to and from the University may be
subject to requests for disclosure by 3rd parties under relevant legislation. The University
of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726
and VAT registered number GB672390524.The primary contact address for the University of Ulster
in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA





________________________________________



This email and any attachments are confidential and intended solely for the use of the addressee
and may contain information which is covered by legal, professional or other privilege. If
you have received this email in error please notify the system manager at postmaster@ulster.ac.uk
and delete this email immediately. Any views or opinions expressed are solely those of the
author and do not necessarily represent those of the University of Ulster. The University's
computer systems may be monitored and communications carried out on them may be recorded to
secure the effective operation of the system and for other lawful purposes. The University
of Ulster does not guarantee that this email or any attachments are free from viruses or 100%
secure. Unless expressly stated in the body of a separate attachment, the text of email is
not intended to form a binding contract. Correspondence to and from the University may be
subject to requests for disclosure by 3rd parties under relevant legislation. The University
of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726
and VAT registered number GB672390524.The primary contact address for the University of Ulster
in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA





Mime
View raw message