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From giri vara prasad nambari <girinamb...@gmail.com>
Subject Re: concept identification query
Date Fri, 12 Apr 2013 16:34:17 GMT
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<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?  ****
>
>  ****
>
>  ****
>
>  ****
>  ------------------------------
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> 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 ****
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