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 C5B6E19F72 for ; Tue, 29 Mar 2016 11:10:48 +0000 (UTC) Received: (qmail 10672 invoked by uid 500); 29 Mar 2016 11:10:48 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 10615 invoked by uid 500); 29 Mar 2016 11:10:48 -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 10595 invoked by uid 99); 29 Mar 2016 11:10:48 -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 11:10:48 +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 B376D1A119C for ; Tue, 29 Mar 2016 11:10:47 +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 C0SnR6AkUYiG for ; Tue, 29 Mar 2016 11:10:46 +0000 (UTC) Received: from GWS06.hcl.com (gws06.hcl.com [203.105.185.25]) by mx1-lw-us.apache.org (ASF Mail Server at mx1-lw-us.apache.org) with ESMTPS id C9E505F238 for ; Tue, 29 Mar 2016 11:10:44 +0000 (UTC) X-IronPort-AV: E=Sophos;i="5.24,410,1454956200"; d="scan'208,217";a="190571039" Received: from unknown (HELO NDA-CORP-HT03.CORP.HCL.IN) ([10.248.64.35]) by GWS06.hcl.com with ESMTP/TLS/AES128-SHA; 29 Mar 2016 16:12:17 +0530 Received: from NDA-HCLC-CSHT06.HCLC.CORP.HCL.IN (10.33.64.81) by NDA-CORP-HT03.CORP.HCL.IN (10.248.64.35) with Microsoft SMTP Server (TLS) id 14.3.235.1; Tue, 29 Mar 2016 16:40:12 +0530 Received: from NDA-HCLC-MBS03.HCLC.CORP.HCL.IN ([10.33.64.34]) by NDA-HCLC-CSHT06.HCLC.CORP.HCL.IN ([::1]) with mapi id 14.03.0235.001; Tue, 29 Mar 2016 16:40:12 +0530 From: Stuti Awasthi To: "'user@ctakes.apache.org'" Subject: RE: Integrate cTakes with latest UMLS DB Thread-Topic: Integrate cTakes with latest UMLS DB Thread-Index: AdGI0S2ktCMXaLHURviexYLuj0bjiQA2lBgA Date: Tue, 29 Mar 2016 11:10:11 +0000 Message-ID: <2270F3695BF2C04DB9FE975FB546FF3C43604AC1@NDA-HCLC-MBS03.hclc.corp.hcl.in> References: <2270F3695BF2C04DB9FE975FB546FF3C43603629@NDA-HCLC-MBS03.hclc.corp.hcl.in> In-Reply-To: <2270F3695BF2C04DB9FE975FB546FF3C43603629@NDA-HCLC-MBS03.hclc.corp.hcl.in> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [10.248.64.135] Content-Type: multipart/alternative; boundary="_000_2270F3695BF2C04DB9FE975FB546FF3C43604AC1NDAHCLCMBS03hcl_" MIME-Version: 1.0 --_000_2270F3695BF2C04DB9FE975FB546FF3C43604AC1NDAHCLCMBS03hcl_ Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable 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@ctakes.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; +--------------------------+ | Tables_in_umls | +--------------------------+ | AMBIGLUI | | AMBIGSUI | | DELETEDCUI | | DELETEDLUI | | DELETEDSUI ...... | SRSTRE1 | | SRSTRE2 | Now im not able to find any step by step guide to integrate cTakes with uml= s database. Here is what I have done : 1) Modified DictionaryLookupAnnotatorDB.xml with jdbc url of my database al= ong with username and password. Now I believe I also need to modify LookupDesc_DB.xml with some umls tablen= ame 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 integra= tion with UMLS. Thanks &Regards Stuti Awasthi ::DISCLAIMER:: ---------------------------------------------------------------------------= ------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and inte= nded for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as informa= tion could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in trans= mission. 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, disse= mination, 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. ---------------------------------------------------------------------------= ------------------------------------------------------------------------- --_000_2270F3695BF2C04DB9FE975FB546FF3C43604AC1NDAHCLCMBS03hcl_ Content-Type: text/html; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable

Hi All,

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

 

Thanks= &Regards

Stuti = Awasthi

&= nbsp;

 

From: Stuti Aw= asthi
Sent: Monday, March 28, 2016 2:46 PM
To: user@ctakes.apache.org
Subject: Integrate cTakes with latest UMLS DB

 

Hi All,

I have been exploring cTakes and wanted to use lates= t 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;

+--------------------------+

| Tables_in_umls      =      |

+--------------------------+

| AMBIGLUI       =           |

| AMBIGSUI       =           |

| DELETEDCUI      &nbs= p;        |

| DELETEDLUI      &nbs= p;        |

| DELETEDSUI  

……

| SRSTRE1       &= nbsp;          |

| SRSTRE2       &= nbsp;          |

 

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

Here is what I have done :

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

 

Now I believe I also need to modify LookupDesc_DB.xm= l 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 execu= ting clinical pipeline with umls database.

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

 

Thanks &Regards

Stuti Awasthi

 



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The contents of thi= s 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, destr= oyed, arrive late or incomplete, or may contain viruses in transmission. Th= e e mail and its contents
(with or without referred errors) shall there= fore not attach any liability on the originator or HCL or its affiliates. <= br>Views or opinions, if any, presented in this email are solely those of t= he author and may not necessarily reflect the
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HCL is= strictly prohibited. If you have received this email in error please delet= e 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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