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From Tim Miller <timothy.mil...@childrens.harvard.edu>
Subject Re: concept identification query
Date Fri, 12 Apr 2013 16:19:02 GMT
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 
> <mailto: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 
> <mailto:nf.rooney@ulster.ac.uk>]
> *Sent:* Friday, April 12, 2013 10:26 AM
> *To:* user@ctakes.apache.org <mailto: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 
> <mailto:Pei.Chen@childrens.harvard.edu>]
> *Sent:* 12 April 2013 15:10
> *To:* <user@ctakes.apache.org <mailto: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 
> <mailto: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 <mailto: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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