Return-Path: X-Original-To: apmail-ctakes-user-archive@www.apache.org Delivered-To: apmail-ctakes-user-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 6B27BF660 for ; Fri, 12 Apr 2013 14:59:43 +0000 (UTC) Received: (qmail 65724 invoked by uid 500); 12 Apr 2013 14:59:43 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 65698 invoked by uid 500); 12 Apr 2013 14:59:43 -0000 Mailing-List: contact user-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: user@ctakes.apache.org Delivered-To: mailing list user@ctakes.apache.org Received: (qmail 65688 invoked by uid 99); 12 Apr 2013 14:59:43 -0000 Received: from athena.apache.org (HELO athena.apache.org) (140.211.11.136) by apache.org (qpsmtpd/0.29) with ESMTP; Fri, 12 Apr 2013 14:59:43 +0000 X-ASF-Spam-Status: No, hits=2.2 required=5.0 tests=HTML_MESSAGE,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (athena.apache.org: domain of Guergana.Savova@childrens.harvard.edu designates 134.174.13.92 as permitted sender) Received: from [134.174.13.92] (HELO mailsmtp2.childrenshospital.org) (134.174.13.92) by apache.org (qpsmtpd/0.29) with ESMTP; Fri, 12 Apr 2013 14:59:33 +0000 Received: from pps.filterd (mailsmtp2.childrenshospital.org [127.0.0.1]) by mailsmtp2.childrenshospital.org (8.14.5/8.14.5) with SMTP id r3CEsCug029335 for ; Fri, 12 Apr 2013 10:59:01 -0400 Received: from smtpndc2.chboston.org (smtpndc2.chboston.org [10.20.50.105]) by mailsmtp2.childrenshospital.org with ESMTP id 1bp352k980-1 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 12 Apr 2013 10:59:00 -0400 Received: from pps.filterd (smtpndc2.chboston.org [127.0.0.1]) by smtpndc2.chboston.org (8.14.5/8.14.5) with SMTP id r3CEtTMZ022532 for ; Fri, 12 Apr 2013 10:59:00 -0400 Received: from chexhubcasbdc2.chboston.org (chexhubcasbdc2.chboston.org [10.20.18.93]) by smtpndc2.chboston.org with ESMTP id 1bp1suj9t3-1 (version=TLSv1/SSLv3 cipher=AES128-SHA bits=128 verify=NOT) for ; Fri, 12 Apr 2013 10:59:00 -0400 Received: from CHEXMBX3A.CHBOSTON.ORG ([fe80::8df1:9966:b0b0:841d]) by CHEXHUBCASBDC2.CHBOSTON.ORG ([::1]) with mapi id 14.02.0309.002; Fri, 12 Apr 2013 10:59:00 -0400 From: "Savova, Guergana" To: "user@ctakes.apache.org" Subject: RE: concept identification query Thread-Topic: concept identification query Thread-Index: Ac43baEXlYVH+8nUSI2FIlp1sGrNjQANPmcA///JsvGAAEdVgIAAOfXA Date: Fri, 12 Apr 2013 14:58:59 +0000 Message-ID: References: <8B2F19897C416A40BA17E6D7E983C4870538B382@UUJ-MBOX-01.ad.ulster.ac.uk>,<51680B14.2030500@childrens.harvard.edu> <8F30AA4B-946D-41B1-8180-39D8E5A25DF5@childrens.harvard.edu> <8B2F19897C416A40BA17E6D7E983C4870538B41F@UUJ-MBOX-01.ad.ulster.ac.uk> In-Reply-To: <8B2F19897C416A40BA17E6D7E983C4870538B41F@UUJ-MBOX-01.ad.ulster.ac.uk> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [172.18.21.55] Content-Type: multipart/alternative; boundary="_000_E5A9FA5ABBF1CA4085D4F0794852A51E20FFDE99CHEXMBX3ACHBOST_" MIME-Version: 1.0 X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10432:5.10.8626,1.0.431,0.0.0000 definitions=2013-04-12_06:2013-04-12,2013-04-12,1970-01-01 signatures=0 X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10432:5.10.8626,1.0.431,0.0.0000 definitions=2013-04-12_06:2013-04-12,2013-04-12,1970-01-01 signatures=0 X-Virus-Checked: Checked by ClamAV on apache.org --_000_E5A9FA5ABBF1CA4085D4F0794852A51E20FFDE99CHEXMBX3ACHBOST_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable You would need to get a UMLS license to get the full functionality. It take= s 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: 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" > wrote: Niall, I'm sure Pei will get back to you soon, but just wanted to let you know, ma= ny of those entities will be found by the standard ctakes installation. I g= et aphasia and stomach. It does not get blood pressure, I think because th= is is filtered out by UMLS semantic class - I think it is categorized as a = "measurement," and cTAKES will find things like disease/disorder, signs/sym= ptoms, and a few others, which this does not fit into exactly. It may be w= orth 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 s= ome 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 ex= ample 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 activi= ty 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 hel= p promote weight gain. She agrees with the plan and has my number for further assessment. May wan= t a Metabolic Rate as well. She takes Codeine a day for knee and stomach pa= in. Original entities and concepts are identified such as "Hyperlidemia" , "kne= e","pain". However concepts associated with addition to the text are not id= entified such as "Aphasia", "blood pressure", "stomach". Also "metabolic r= ate" 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 t= hose 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 Un= iversity of Ulster does not guarantee that this email or any attachments ar= e 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 reque= sts for disclosure by 3rd parties under relevant legislation. The Universit= y of Ulster was founded by Royal Charter in 1984 and is registered with com= pany number RC000726 and VAT registered number GB672390524.The primary cont= act address for the University of Ulster in Northern Ireland is,Cromore Roa= d, 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 t= hose 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 Un= iversity of Ulster does not guarantee that this email or any attachments ar= e 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 reque= sts for disclosure by 3rd parties under relevant legislation. The Universit= y of Ulster was founded by Royal Charter in 1984 and is registered with com= pany number RC000726 and VAT registered number GB672390524.The primary cont= act address for the University of Ulster in Northern Ireland is,Cromore Roa= d, Coleraine, Co. Londonderry BT52 1SA --_000_E5A9FA5ABBF1CA4085D4F0794852A51E20FFDE99CHEXMBX3ACHBOST_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

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

Hope this helps.<= /o:p>

--Guergana<= /span>

 

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,

 <= /span>

I don&#= 8217;t have a UMLS license yet but thanks for looking into this.

 <= /span>

From: Chen, Pe= i [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, ma= ny of those entities will be found by the standard ctakes installation. I g= et aphasia and stomach.  It does not get blood pressure, I think becau= se 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%&quo= t;, 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 conc= ept identification.  I have modifying the example text given in the in= stallation instructions to demonstrate the use of CAS Visual Debugger.=

 

My text is:

 

Dr. Nutritious=

 

Medical Nutrition The= rapy for Hyperlipidemia and Aphasia<= /span>

 

Referral from: Julie = Tester, RD, LD, CNSD

Phone contact: (555) = 555-1212

Height: 144 cm &= nbsp; Current Weight: 45 kg   Date of current weight: 02-29-2001&= nbsp;  Admit Weight:  53 kg   BMI: 18 kg/m2

Diet: General<= span lang=3D"EN-GB">

Daily Calorie needs (= kcals): 1500 calories, assessed as HB + 20% for activity and blood pres= sure.

Daily Protein needs: = 40 grams,  assessed as 1.0 g/kg.

Pt has been on a 3-da= y calorie count and has had an average intake of 1100 calories.  She w= as 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 Ra= te as well. She takes Codeine a day for knee and stomach pain.

 

 

Original entities and concepts = are identified such as “Hyperlidemia” , “knee”,R= 20;pain”. However concepts associated with addition to the text are n= ot 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 con= fidential 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 syst= em manager at postmaster@ulster.ac.uk and = delete this email immediately. Any views or opinions expressed are solely t= hose 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 rec= orded to secure the effective operation of the system and for other lawful = purposes. The University of Ulster does not guarantee that this email or an= y attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachme= nt, the text of email is not intended to form a binding contract. Correspon= dence 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 regis= tered with company number RC000726 and VAT registered number GB672390524.Th= e 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 con= fidential 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 syst= em manager at postmaster@ulster.ac.uk and = delete this email immediately. Any views or opinions expressed are solely t= hose 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 rec= orded to secure the effective operation of the system and for other lawful = purposes. The University of Ulster does not guarantee that this email or an= y attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachme= nt, the text of email is not intended to form a binding contract. Correspon= dence 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 regis= tered with company number RC000726 and VAT registered number GB672390524.Th= e primary contact address for the University of Ulster in Northern Ireland = is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA

--_000_E5A9FA5ABBF1CA4085D4F0794852A51E20FFDE99CHEXMBX3ACHBOST_--