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 604B21901C for ; Tue, 29 Mar 2016 11:40:42 +0000 (UTC) Received: (qmail 75151 invoked by uid 500); 29 Mar 2016 11:40:37 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 75121 invoked by uid 500); 29 Mar 2016 11:40:37 -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 75107 invoked by uid 99); 29 Mar 2016 11:40:36 -0000 Received: from pnap-us-west-generic-nat.apache.org (HELO spamd2-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 29 Mar 2016 11:40:36 +0000 Received: from localhost (localhost [127.0.0.1]) by spamd2-us-west.apache.org (ASF Mail Server at spamd2-us-west.apache.org) with ESMTP id 86F571A59A6 for ; Tue, 29 Mar 2016 11:40:36 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd2-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: 1.998 X-Spam-Level: * X-Spam-Status: No, score=1.998 tagged_above=-999 required=6.31 tests=[HTML_MESSAGE=2, RCVD_IN_DNSWL_NONE=-0.0001, RP_MATCHES_RCVD=-0.001, SPF_PASS=-0.001] autolearn=disabled Received: from mx1-lw-us.apache.org ([10.40.0.8]) by localhost (spamd2-us-west.apache.org [10.40.0.9]) (amavisd-new, port 10024) with ESMTP id 1gcwmbOqkaMs for ; Tue, 29 Mar 2016 11:40:34 +0000 (UTC) Received: from zixvpm.geisinger.edu (zixvpm01.geisinger.edu [159.240.9.8]) by mx1-lw-us.apache.org (ASF Mail Server at mx1-lw-us.apache.org) with ESMTPS id C3A505F471 for ; Tue, 29 Mar 2016 11:40:33 +0000 (UTC) Received: from 127.0.0.1 (ZixVPM [127.0.0.1]) by Outbound.geisinger.edu (Proprietary) with SMTP id 35C16D017CF for ; Tue, 29 Mar 2016 07:40:27 -0400 (EDT) Received: from LOFEXMBX207W12V.geisinger.edu (ghsnetprew8k1v.geisinger.edu [10.230.9.96]) by zixvpm.geisinger.edu (Proprietary) with ESMTP id 1F4C0D26CFB for ; Tue, 29 Mar 2016 07:40:27 -0400 (EDT) Received: from LOFEXMBX207W12V.geisinger.edu (10.240.245.19) by LOFEXMBX207W12V.geisinger.edu (10.240.245.19) with Microsoft SMTP Server (TLS) id 15.0.1156.6; Tue, 29 Mar 2016 07:40:26 -0400 Received: from LOFEXMBX207W12V.geisinger.edu ([fe80::3464:515c:5d48:2220]) by LOFEXMBX207W12V.geisinger.edu ([fe80::3464:515c:5d48:2220%12]) with mapi id 15.00.1156.000; Tue, 29 Mar 2016 07:40:26 -0400 From: "Geise, Brandon D." To: "user@ctakes.apache.org" Subject: RE: Integrate cTakes with latest UMLS DB Thread-Topic: Integrate cTakes with latest UMLS DB Thread-Index: AdGI0S2ktCMXaLHURviexYLuj0bjiQA2lBgAAAC6EUA= Date: Tue, 29 Mar 2016 11:40:26 +0000 Message-ID: <8c07713ae70d40d2a9f44a390a06e514@LOFEXMBX207W12V.geisinger.edu> References: <2270F3695BF2C04DB9FE975FB546FF3C43603629@NDA-HCLC-MBS03.hclc.corp.hcl.in> <2270F3695BF2C04DB9FE975FB546FF3C43604AC1@NDA-HCLC-MBS03.hclc.corp.hcl.in> In-Reply-To: <2270F3695BF2C04DB9FE975FB546FF3C43604AC1@NDA-HCLC-MBS03.hclc.corp.hcl.in> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-ms-exchange-transport-fromentityheader: Hosted x-originating-ip: [10.240.245.250] Content-Type: multipart/alternative; boundary="_000_8c07713ae70d40d2a9f44a390a06e514LOFEXMBX207W12Vgeisinge_" MIME-Version: 1.0 X-Symantec-Inspected: Forwarded X-VPM-MSG-ID: f1a4a9fe-b8f0-45bb-b4cf-846487ff957d X-VPM-HOST: zixvpm01.geisinger.edu X-VPM-GROUP-ID: 329ffbfa-2ec3-4417-a159-164794bef965 X-VPM-ENC-REGIME: Plaintext X-VPM-IS-HYBRID: 0 --_000_8c07713ae70d40d2a9f44a390a06e514LOFEXMBX207W12Vgeisinge_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Stuti, Depending on the dictionary implementation you chose (fast vs older) will = depend on which table(s) you'll need to create. For the older dictionary = version you'd need to create a table using the first word method. The = newer fast dictionary relies on a rare word approach. I'm not sure of all = the details but you'd need to create table that has the same information. = If you're just exploring one thought would be to use the Dictionary GUI = tool, https://svn.apache.org/repos/asf/ctakes/sandbox/dictionary-gui/, = create the new fast dictionary 2015AB dictionary in a hsql format. Hopefully that helps some. Thanks, Brandon From: Stuti Awasthi =5Bmailto:stutiawasthi=40hcl.com=5D Sent: Tuesday, March 29, 2016 7:10 AM To: 'user=40ctakes.apache.org' Subject: RE: Integrate cTakes with latest UMLS DB Hi All, Any help will be good. Im still waiting for some response. Thanks &Regards Stuti Awasthi From: Stuti Awasthi Sent: Monday, March 28, 2016 2:46 PM To: user=40ctakes.apache.org Subject: Integrate cTakes with latest UMLS DB Hi All, I have been exploring cTakes and wanted to use latest UMLS 2015ab with it. = To achieve the same, I have installed UMLS in mysql database. Database Name: umls Numbers of Tables created : 53 Eg : mysql> show tables; +--------------------------+ =7C Tables_in_umls =7C +--------------------------+ =7C AMBIGLUI =7C =7C AMBIGSUI =7C =7C DELETEDCUI =7C =7C DELETEDLUI =7C =7C DELETEDSUI =2E..... =7C SRSTRE1 =7C =7C SRSTRE2 =7C Now im not able to find any step by step guide to integrate cTakes with = umls database. Here is what I have done : 1) Modified DictionaryLookupAnnotatorDB.xml with jdbc url of my database = along with username and password. Now I believe I also need to modify LookupDesc_DB.xml with some umls = tablename which can get cui, tui and text info. I need some help , which table should I be pointing to lookup ? Also after = is there any other step or I should be good in executing clinical pipeline = with umls database. Also please point some steps guide/document of available for cTakes = integration with UMLS. Thanks &Regards Stuti Awasthi ::DISCLAIMER:: ---------------------------------------------------------------------------= ------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and = intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as = information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in = transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability = on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the = author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, = dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior = written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error = please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses = and other defects. ---------------------------------------------------------------------------= ------------------------------------------------------------------------- IMPORTANT WARNING: The information in this message (and the documents = attached to it, if any) is confidential and may be legally privileged. It = is intended solely for the addressee. Access to this message by anyone = else is unauthorized. If you are not the intended recipient, any = disclosure, copying, distribution or any action taken, or omitted to be = taken, in reliance on it is prohibited and may be unlawful. If you have = received this message in error, please delete all electronic copies of = this message (and the documents attached to it, if any), destroy any hard = copies you may have created and notify me immediately by replying to this = email. Thank you. Geisinger Health System utilizes an encryption process to safeguard = Protected Health Information and other confidential data contained in = external e-mail messages. If email is encrypted, the recipient will = receive an e-mail instructing them to sign on to the Geisinger Health = System Secure E-mail Message Center to retrieve the encrypted e-mail.= --_000_8c07713ae70d40d2a9f44a390a06e514LOFEXMBX207W12Vgeisinge_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable <=21--=5Bif gte mso 9=5D> <=21=5Bendif=5D--><=21--=5Bif gte mso 9=5D> <=21=5Bendif=5D-->

Hi = Stuti,

 

Depending = on the dictionary implementation you chose (fast vs older) will depend on = which table(s) you&=238217;ll need to create.  For the older = dictionary version you&=238217;d need to create a table using the first = word method.  The newer fast dictionary relies on a rare word approach.  = I&=238217;m not sure of all the details but you&=238217;d need to create = table that has the same information.  If you&=238217;re just = exploring one thought would be to use the Dictionary GUI tool, https://svn.apache.org/repos/asf/ctakes/sandbox/dictionary-gui/, = create the new fast dictionary 2015AB dictionary in a hsql = format.

 

Hopefully = that helps some.

 

Thanks,

Brandon

 

 

From: Stuti Awasthi = =5Bmailto:stutiawasthi=40hcl.com=5D
Sent: Tuesday, March 29, 2016 7:10 AM
To: 'user=40ctakes.apache.org' <user=40ctakes.apache.org>
Subject: RE: Integrate cTakes with latest UMLS DB

 

Hi = All,

Any help = will be good. Im still waiting for some response.

 

Thanks = &Regards

Stuti = Awasthi

 

 

Fr= om: = Stuti Awasthi
Sent: Monday, March 28, 2016 2:46 PM
To: user=40ctakes.apache.org Subject: Integrate cTakes with latest UMLS DB

 

Hi All,

I have been exploring cTakes and wanted to use = latest UMLS 2015ab with it. To achieve the same, I have installed UMLS in = mysql database.

 

Database Name: umls

Numbers of Tables created : 53

Eg : mysql> show tables;

&=2343;--------------------------&=2343;=

=7C = Tables_in_umls           = =7C

&=2343;--------------------------&=2343;=

=7C = AMBIGLUI           &= nbsp;     =7C

=7C = AMBIGSUI           &= nbsp;     =7C

=7C = DELETEDCUI           = ;    =7C

=7C = DELETEDLUI           = ;    =7C

=7C DELETEDSUI  

&=238230;&=238230;

=7C = SRSTRE1           &n= bsp;      =7C

=7C = SRSTRE2           &n= bsp;      =7C

 

Now im not able to find any step by step guide = to integrate cTakes with umls database.

Here is what I have done :

1) Modified DictionaryLookupAnnotatorDB.xml = with jdbc url of my database along with username and = password.

 

Now I believe I also need to modify = LookupDesc_DB.xml with some umls tablename which can get cui, tui and text = info.

I need some help , which table should I be = pointing to lookup ? Also after is there any other step or I should be = good in executing clinical pipeline with umls database.

Also please point some steps guide/document of = available for cTakes integration with UMLS.

 

Thanks &Regards

Stuti Awasthi

 



::DISCLAIMER::
---------------------------------------------------------------------------= -------------------------------------------------------------------------

The contents of this e-mail and any attachment(s) are confidential = and intended for the named recipient(s) only.
E-mail transmission is not guaranteed to be secure or error-free as = information could be intercepted, corrupted,
lost, destroyed, arrive late or incomplete, or may contain viruses in = transmission. The e mail and its contents
(with or without referred errors) shall therefore not attach any liability = on the originator or HCL or its affiliates.
Views or opinions, if any, presented in this email are solely those of the = author and may not necessarily reflect the
views or opinions of HCL or its affiliates. Any form of reproduction, = dissemination, copying, disclosure, modification,
distribution and / or publication of this message without the prior = written consent of authorized representative of
HCL is strictly prohibited. If you have received this email in error = please delete it and notify the sender immediately.
Before opening any email and/or attachments, please check them for viruses = and other defects.

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IMPORTANT WARNING

IMPORTANT WARNING: The information in this message (and the documents = attached to it, if any) is confidential and may be legally privileged. It = is intended solely for the addressee. Access to this message by anyone = else is unauthorized. If you are not the intended recipient, any = disclosure, copying, distribution or any action taken, or omitted to be = taken, in reliance on it is prohibited and may be unlawful. If you have = received this message in error, please delete all electronic copies of = this message (and the documents attached to it, if any), destroy any hard = copies you may have created and notify me immediately by replying to this = email. Thank you. Geisinger Health System utilizes an encryption process to safeguard = Protected Health Information and other confidential data contained in = external e-mail messages. If email is encrypted, the recipient will = receive an e-mail instructing them to sign on to the Geisinger Health = System Secure E-mail Message Center to retrieve the encrypted e-mail.

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