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 83CB9190D4 for ; Tue, 29 Mar 2016 12:05:39 +0000 (UTC) Received: (qmail 43201 invoked by uid 500); 29 Mar 2016 12:05:39 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 43172 invoked by uid 500); 29 Mar 2016 12:05:39 -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 43162 invoked by uid 99); 29 Mar 2016 12:05:38 -0000 Received: from pnap-us-west-generic-nat.apache.org (HELO spamd4-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 29 Mar 2016 12:05:38 +0000 Received: from localhost (localhost [127.0.0.1]) by spamd4-us-west.apache.org (ASF Mail Server at spamd4-us-west.apache.org) with ESMTP id 88CBEC0315 for ; Tue, 29 Mar 2016 12:05:38 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd4-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 mx2-lw-eu.apache.org ([10.40.0.8]) by localhost (spamd4-us-west.apache.org [10.40.0.11]) (amavisd-new, port 10024) with ESMTP id bBhUjMP8k6kX for ; Tue, 29 Mar 2016 12:05:34 +0000 (UTC) Received: from GWS05.hcl.com (gws05.hcl.com [203.105.185.23]) by mx2-lw-eu.apache.org (ASF Mail Server at mx2-lw-eu.apache.org) with ESMTPS id 1BA305FAEE for ; Tue, 29 Mar 2016 12:05:32 +0000 (UTC) X-IronPort-AV: E=Sophos;i="5.24,410,1454956200"; d="scan'208,217";a="156685597" Received: from unknown (HELO NDA-CORP-HT02.CORP.HCL.IN) ([10.248.64.34]) by GWS05.hcl.com with ESMTP/TLS/AES128-SHA; 29 Mar 2016 17:30:41 +0530 Received: from NDA-HCLC-CSHT06.HCLC.CORP.HCL.IN (10.33.64.81) by NDA-CORP-HT02.CORP.HCL.IN (10.248.64.34) with Microsoft SMTP Server (TLS) id 14.3.235.1; Tue, 29 Mar 2016 17:35:25 +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 17:35:25 +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: AdGI0S2ktCMXaLHURviexYLuj0bjiQA2lBgAAAEGiEAAAGYKQAAAaxtuAAAMiDA= Date: Tue, 29 Mar 2016 12:05:23 +0000 Message-ID: <2270F3695BF2C04DB9FE975FB546FF3C43604B5C@NDA-HCLC-MBS03.hclc.corp.hcl.in> References: <2270F3695BF2C04DB9FE975FB546FF3C43603629@NDA-HCLC-MBS03.hclc.corp.hcl.in> <2270F3695BF2C04DB9FE975FB546FF3C43604AC1@NDA-HCLC-MBS03.hclc.corp.hcl.in> ,<2270F3695BF2C04DB9FE975FB546FF3C43604B3B@NDA-HCLC-MBS03.hclc.corp.hcl.in> <5d82bfa8b2ec447eb04965cdc254de1d@LOFEXMBX207W12V.geisinger.edu> In-Reply-To: <5d82bfa8b2ec447eb04965cdc254de1d@LOFEXMBX207W12V.geisinger.edu> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [10.33.64.124] Content-Type: multipart/alternative; boundary="_000_2270F3695BF2C04DB9FE975FB546FF3C43604B5CNDAHCLCMBS03hcl_" MIME-Version: 1.0 --_000_2270F3695BF2C04DB9FE975FB546FF3C43604B5CNDAHCLCMBS03hcl_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Thanks Brandon, then I will check dictionary-gui tool and try to use it and= will get back with queries if any. Regards Stuti Awasthi From: Geise, Brandon D. [mailto:bdgeise@geisinger.edu] Sent: Tuesday, March 29, 2016 5:32 PM To: Stuti Awasthi; 'user@ctakes.apache.org' Subject: RE: Integrate cTakes with latest UMLS DB Hi Stuti, Unless someone else has created another solution the current Dictionary Gui= tool doesn't have this support yet. It's something that I plan to work on= in the future for the GUI tool. Thanks, Brandon Sent from Mail for Window= s 10 From: Stuti Awasthi Sent: Tuesday, March 29, 2016 7:59 AM To: 'user@ctakes.apache.org' Subject: RE: Integrate cTakes with latest UMLS DB Thanks Brandon, Jessica for response. I will look at dictionary tools as me= ntioned and will try to figure out how it can be used for my purpose. I wil= l certainly get back on mailing list with more queries if any. As of now with limited understanding, I understand that current UMLS2015 da= tabase will be converted to hsql format which I can use in the pipeline by = changing configurations in required XMLs. One more query, cTakes also prov= ides "DictionaryLookupAnnotatorDB" which is supposed to be used if we want = to connect to required tables in umls database. Please correct my understan= ding but do we have similar tool/script to be execute on umls database to g= enerate the required format table "umls2015ab" which can be directly includ= ed in dictionary lookup. Thanks for the help! Regards Stuti Awasthi From: Glover, Jessica [mailto:Jessica.Glover@ssa.gov] Sent: Tuesday, March 29, 2016 5:17 PM To: 'user@ctakes.apache.org' Subject: RE: Integrate cTakes with latest UMLS DB Hi Stuti, One thing to note about the dictionary tool is that it is still in sandbox = mode, so there is no official documentation or step-by-step guide for it. H= owever, it contains a readme, and it has been discussed on the mailing list= , so you can search the archive for that "documentation." Searchable cTakes mailing list archive: http://ctakes.markmail.org/search/ Regards, Jessica From: Stuti Awasthi [mailto:stutiawasthi@hcl.com] Sent: Tuesday, March 29, 2016 7:10 AM To: 'user@ctakes.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@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. ---------------------------------------------------------------------------= ------------------------------------------------------------------------- ________________________________ IMPORTANT WARNING: The information in this message (and the documents attac= hed to it, if any) is confidential and may be legally privileged. It is int= ended solely for the addressee. Access to this message by anyone else is un= authorized. If you are not the intended recipient, any disclosure, copying,= distribution or any action taken, or omitted to be taken, in reliance on i= t is prohibited and may be unlawful. If you have received this message in e= rror, please delete all electronic copies of this message (and the document= s 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 Heal= th System utilizes an encryption process to safeguard Protected Health Info= rmation and other confidential data contained in external e-mail messages. = If email is encrypted, the recipient will receive an e-mail instructing the= m to sign on to the Geisinger Health System Secure E-mail Message Center to= retrieve the encrypted e-mail. --_000_2270F3695BF2C04DB9FE975FB546FF3C43604B5CNDAHCLCMBS03hcl_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable IMPORTANT WARNING

Thanks Brandon, then I= will check dictionary-gui tool and try to use it and will get back with qu= eries if any.

 

Regards

Stuti Awasthi

From: Geise, B= randon D. [mailto:bdgeise@geisinger.edu]
Sent: Tuesday, March 29, 2016 5:32 PM
To: Stuti Awasthi; 'user@ctakes.apache.org'
Subject: RE: Integrate cTakes with latest UMLS DB<= /p>

 

Hi Stuti,

 

Unless someone else has created another solution the= current Dictionary Gui tool doesn’t have this support yet.  It&= #8217;s something that I plan to work on in the future for the GUI tool.&nb= sp;

 

Thanks,

Brandon

 

Sent from Mail for Windows 10

 

From: Stuti Awasthi
Sent: Tuesday, March 29, 2016 7:59 AM
To: 'user@ctakes.apache.or= g'
Subject: RE: Integrate cTakes with latest UMLS DB

 

Thanks Brandon, Jessic= a for response. I will look at dictionary tools as mentioned and will try t= o figure out how it can be used for my purpose. I will certainly get back o= n mailing list with more queries if any.

 

As of now with limited= understanding, I understand that current UMLS2015 database will be convert= ed to hsql format which I can use in the pipeline by changing configuration= s in required XMLs.  One more query, cTakes also provides “DictionaryLookupAnnotatorDB” whic= h is supposed to be used if we want to connect to required tables in umls d= atabase. Please correct my understanding but do we have similar tool/script= to be execute on umls database to generate the required format table “umls2015ab” which can be directly i= ncluded in dictionary lookup.

 

Thanks for the help!

 

Regards

Stuti Awasthi

 

From: Glover, = Jessica [mailto:Jessica.Glover@ss= a.gov]
Sent: Tuesday, March 29, 2016 5:17 PM
To: 'user@ctakes.apache.org'
Subject: RE: Integrate cTakes with latest UMLS DB<= /p>

 

Hi Stuti,<= /o:p>

 

One thing to note abou= t the dictionary tool is that it is still in sandbox mode, so there is no o= fficial documentation or step-by-step guide for it. However, it contains a = readme, and it has been discussed on the mailing list, so you can search the archive for that “documentat= ion.”

 

Searchable cTakes mail= ing list archive: http://ctakes.markmail.org/s= earch/

 

Regards, <= /o:p>

Jessica

 

 

Hi All,

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

 

Thanks= &Regards

Stuti = Awasthi

 =

 

 

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

 



::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 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.

-------------------------------= ---------------------------------------------------------------------------= ------------------------------------------

 

IMPORTANT WARNING: The information in this message (and the documents at= tached 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 ta= ken, or omitted to be taken, in reliance on it is prohibited and may be unl= awful. If you have received this message in error, please delete all electr= onic copies of this message (and the documents attached to it, if any), destroy any hard copies you may hav= e created and notify me immediately by replying to this email. Thank you. G= eisinger Health System utilizes an encryption process to safeguard Protecte= d Health Information and other confidential data contained in external e-mail messages. If email is encrypted, the rec= ipient 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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