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 68EDB1992E for ; Tue, 5 Apr 2016 11:43:07 +0000 (UTC) Received: (qmail 11231 invoked by uid 500); 5 Apr 2016 11:43:07 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 11192 invoked by uid 500); 5 Apr 2016 11:43:07 -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 11182 invoked by uid 99); 5 Apr 2016 11:43:06 -0000 Received: from pnap-us-west-generic-nat.apache.org (HELO spamd3-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 05 Apr 2016 11:43:06 +0000 Received: from localhost (localhost [127.0.0.1]) by spamd3-us-west.apache.org (ASF Mail Server at spamd3-us-west.apache.org) with ESMTP id 60A44180542 for ; Tue, 5 Apr 2016 11:43:06 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd3-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 (spamd3-us-west.apache.org [10.40.0.10]) (amavisd-new, port 10024) with ESMTP id s0wX96yFSBVq for ; Tue, 5 Apr 2016 11:42:58 +0000 (UTC) Received: from zixvpm.geisinger.edu (zixvpm02.geisinger.edu [159.240.9.22]) by mx1-lw-us.apache.org (ASF Mail Server at mx1-lw-us.apache.org) with ESMTPS id 7FD095F19B for ; Tue, 5 Apr 2016 11:42:58 +0000 (UTC) Received: from 127.0.0.1 (ZixVPM [127.0.0.1]) by Outbound.geisinger.edu (Proprietary) with SMTP id B270D17083D1 for ; Tue, 5 Apr 2016 07:42:51 -0400 (EDT) Received: from LOFEXMBX210W12V.geisinger.edu (ghsnetprew8k2v.geisinger.edu [10.230.9.97]) by zixvpm.geisinger.edu (Proprietary) with ESMTP id 956BF17083D0 for ; Tue, 5 Apr 2016 07:42:51 -0400 (EDT) Received: from LOFEXMBX207W12V.geisinger.edu (10.240.245.19) by LOFEXMBX210W12V.geisinger.edu (10.240.245.22) with Microsoft SMTP Server (TLS) id 15.0.1156.6; Tue, 5 Apr 2016 07:42:51 -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, 5 Apr 2016 07:42:51 -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: AdGI0S2ktCMXaLHURviexYLuj0bjiQA2lBgAAAEGiEAAAGYKQAAAaxtuAAAMiDAAWF85AAAKI6VXAADOrNAAAH8iSADwg5vgAArp8UA= Date: Tue, 5 Apr 2016 11:42:50 +0000 Message-ID: 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> <2270F3695BF2C04DB9FE975FB546FF3C43604B5C@NDA-HCLC-MBS03.hclc.corp.hcl.in>,<2270F3695BF2C04DB9FE975FB546FF3C43608589@NDA-HCLC-MBS03.hclc.corp.hcl.in> <2270F3695BF2C04DB9FE975FB546FF3C43608A38@NDA-HCLC-MBS03.hclc.corp.hcl.in>, <2270F3695BF2C04DB9FE975FB546FF3C43608ADA@NDA-HCLC-MBS03.hclc.corp.hcl.in> <2270F3695BF2C04DB9FE975FB546FF3C4360FAFF@NDA-HCLC-MBS03.hclc.corp.hcl.in> In-Reply-To: <2270F3695BF2C04DB9FE975FB546FF3C4360FAFF@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_f27b695bc57f41f68939d12a7ac92230LOFEXMBX207W12Vgeisinge_" MIME-Version: 1.0 X-Symantec-Inspected: Forwarded X-VPM-MSG-ID: a8c5e422-17d4-4b88-bfc0-dc24e81e56ce X-VPM-HOST: zixvpm02.geisinger.edu X-VPM-GROUP-ID: b6854514-ce9a-45f1-b3e5-6ad105f55d9c X-VPM-ENC-REGIME: Plaintext X-VPM-IS-HYBRID: 0 --_000_f27b695bc57f41f68939d12a7ac92230LOFEXMBX207W12Vgeisinge_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Stuti, Great! Glad you got the dictionary GUI tools working successfully. Are yo= u using the latest ctakes trunk? I know there was a change in some of the = dictionary methods and it appears your XML values are being read in the wro= ng manner. I believe you need to be on 3.2.3 or later. Thanks, Brandon From: Stuti Awasthi [mailto:stutiawasthi@hcl.com] Sent: Tuesday, April 05, 2016 3:32 AM To: user@ctakes.apache.org Subject: RE: Integrate cTakes with latest UMLS DB Hi Brandon, Sorry for coming late on this as I was stuck with some other task. Ok so I = have used Dictionary_Gui with Java 8 and compiled successfully. After that = used the tool to create the hsql data files for my current UMLS2015 and it = generates all the relevant files as described in your post : "CTAKES DICTIO= NARY CREATOR GUI !!!". After generating the dictionary, I wanted to use it with cTakes , so I have= modified "UmlsLookupAnnotator.xml" file:org/apache/ctakes/dictionary/lookup/fast/umls2= 015aa.xml And selected "AggregatePlaintextFastUMLSProcessor" as analysis engine for c= linicalpipeline. Following is the error which Im getting: Error Trace: 05 Apr 2016 11:52:55 INFO JdbcConnectionFactory - Connecting to jdbc:hsqld= b:file:resources/org/apache/ctakes/dictionary/lookup/fast/umls2015aa/umls20= 15aa: .................................................. 50 .................................................. 100 .................................................. 150 .................... 05 Apr 2016 11:53:52 INFO JdbcConnectionFactory - Database connected 05 Apr 2016 11:53:53 ERROR JdbcConceptFactory - Could not create Concept Da= ta Selection Call java.sql.SQLException: Table not found in statement [SELECT * FROM long WHE= RE CUI =3D ?] at org.hsqldb.jdbc.Util.throwError(Unknown Source) at org.hsqldb.jdbc.jdbcPreparedStatement.(Unknown Source) at org.hsqldb.jdbc.jdbcConnection.prepareStatement(Unknown Source) at org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory.= createSelectCall(JdbcConceptFactory.java:204) at org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory.= (JdbcConceptFactory.java:83) at org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory.= (JdbcConceptFactory.java:57) at org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFact= ory.(UmlsJdbcConceptFactory.java:30) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Me= thod) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown So= urce) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknow= n Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) Please find attached "umls2015aa.xml" file generated by dictionary_gui tool= . Why Im getting the above mentioned error.. Any ideas/suggestions will be = helpful. Thanks &Regards Stuti Awasthi From: Stuti Awasthi Sent: Thursday, March 31, 2016 5:17 PM To: user@ctakes.apache.org Subject: RE: Integrate cTakes with latest UMLS DB Thanks. Ya I have read the long conversation between you and Sean on how to use dic= tionary tool utility and that really helped. Thanks to Sean. Thanks for java 8 pointer. Presently Im using Java7 and already added libra= ries in build path. Let me try with Java8 and Il come back. Example of error : org.apache.ctakes.dictionary.creator.gui.umls.Concept.ja= va concept.getTuis().stream().forEach( this::addTui ); The method stream() is undefined for the type Collection This is just an example, similarly Im getting more errors in different clas= ses. Thanks Stuti Awasthi ________________________________ From: Geise, Brandon D. [bdgeise@geisinger.edu] Sent: Thursday, March 31, 2016 5:02 PM To: user@ctakes.apache.org Subject: RE: Integrate cTakes with latest UMLS DB Hi Stuti, All credit for the dictionary work goes to Sean Finan. What errors are you= getting? I'm not aware of a precompiled jar. I do remember that I needed= to switch to Java 8, if you aren't already to compile the project. You al= so may need to reference the lib folder or move those jars to the project l= ibrary path in order to compile. Brandon From: Stuti Awasthi [mailto:stutiawasthi@hcl.com] Sent: Thursday, March 31, 2016 7:14 AM To: 'user@ctakes.apache.org' > Subject: RE: Integrate cTakes with latest UMLS DB Hi All, Sorry , I think I got confused with dictionary-gui and dictionary-tool proj= ects. Jessica mentioned about dictionary tool and its README which I follow= ed along with the previous mail threads to generate umls dictionary in file= format. Im still to use this dictionary with cTakes so i might comeback wi= th issues. Also I would like to use dictionary-gui posted by Brandon. When I have chec= kout the code and imported in eclipse, its showing compilation error in cla= sses due to which even I have created the jar of the project, it is not run= ning. Any idea about the compilation errors or if there is a pre built bina= ry which can be used (similar to dictionary tools jar) that would be great. Thanks for your help and patience. Regards Stuti Awasthi ________________________________ From: Stuti Awasthi Sent: Thursday, March 31, 2016 11:58 AM To: 'user@ctakes.apache.org' Subject: RE: Integrate cTakes with latest UMLS DB Hi Brandon, Jessica I lookedup at dictionary-gui utility. Here is what I did : Checkout the so= urce code https://svn.apache.org/repos/asf/ctakes/sandbox/dictionary-gui/ a= nd imported in my eclipse IDE. Now I was not able to find any README with t= his project. Hence I checked the code and found that "CreaterGui.java" migh= t be the mail class to launch the GUI. My queries are : * Is there any README as Jessica mentioned or simply launching the = CreaterGui.java class would be suffice. * Is there any commands to execute tool on linux server (without gn= ome) . Something like command like options? Im asking this because Im worki= ng on linux machine where I have installed lated UMLS2015. Few more questions: * As Brandon mentioned : that I might need to create the tables tha= t will have same information (based on rare /first word approach). Do we kn= ow how to create those tables ?? Any SQL statements or links will be useful= . * I found the following link in Ctakes3.1 documentation but looks l= ike broken. Any clue on redirected path/links * https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=3D28&t= =3D423 * https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=3D28&t= =3D80&start=3D20#p1459 * Can I create full dictionary(not only the fast one) from dictionary t= ool. Thanks &Regards Stuti Awasthi From: Stuti Awasthi Sent: Tuesday, March 29, 2016 5:35 PM To: 'user@ctakes.apache.org' Subject: RE: Integrate cTakes with latest UMLS DB 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. 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Hi Stuti,

 

Great!  Glad you = got the dictionary GUI tools working successfully.  Are you using the = latest ctakes trunk?  I know there was a change in some of the diction= ary methods and it appears your XML values are being read in the wrong manner.  I believe you need to be on 3.2.3 or later= .

 

Thanks,

Brandon

 

From: Stuti Awasthi [mailto:stutiawasthi@hcl.= com]
Sent: Tuesday, April 05, 2016 3:32 AM
To: user@ctakes.apache.org
Subject: RE: Integrate cTakes with latest UMLS DB

 

Hi Brandon,=

 

Sorry for coming late = on this as I was stuck with some other task. Ok so I have used Dictionary_G= ui with Java 8 and compiled successfully. After that used the tool to creat= e the hsql data files for my current UMLS2015 and it generates all the relevant files as described in your post= : “CTAKES DICTIONARY CREATOR GUI !!!”.

 

After generating the d= ictionary, I wanted to use it with cTakes , so I have modified “UmlsL= ookupAnnotator.xml”

<fileResourceSpecifier>

   &nbs= p;           <fileUrl&= gt;file:org/apache/ctakes/dictionary/lookup/fast/umls2015aa.xml</= fileUrl>

   &nbs= p;        </fileResourceSpecifier>=

 

And selected “= ;AggregatePlaintextFastUMLSProcessor” as analysis engine for clin= icalpipeline. Following is the error which Im getting:

Error Trace:

05 Apr 2016 11:52:55&n= bsp; INFO JdbcConnectionFactory - Connecting to jdbc:hsqldb:file:resources/= org/apache/ctakes/dictionary/lookup/fast/umls2015aa/umls2015aa:<= /span>

 

......................= ............................ 50

......................= ............................ 100

......................= ............................ 150

....................

05 Apr 2016 11:53:5= 2  INFO JdbcConnectionFactory -  Database connected

05 Apr 2016 11:53:5= 3 ERROR JdbcConceptFactory - Could not create Concept Data Selection Call

java.sql.SQLExcepti= on: Table not found in statement [SELECT * FROM long WHERE CUI =3D ?]<= /o:p>

   &nbs= p;    at org.hsqldb.jdbc.Util.throwError(Unknown Source)

   &nbs= p;    at org.hsqldb.jdbc.jdbcPreparedStatement.<init>(= Unknown Source)

   &nbs= p;    at org.hsqldb.jdbc.jdbcConnection.prepareStatement(Unk= nown Source)

   &nbs= p;    at org.apache.ctakes.dictionary.lookup2.concept.JdbcCo= nceptFactory.createSelectCall(JdbcConceptFactory.java:204)

   &nbs= p;    at org.apache.ctakes.dictionary.lookup2.concept.JdbcCo= nceptFactory.<init>(JdbcConceptFactory.java:83)

   &nbs= p;    at org.apache.ctakes.dictionary.lookup2.concept.JdbcCo= nceptFactory.<init>(JdbcConceptFactory.java:57)

   &nbs= p;    at org.apache.ctakes.dictionary.lookup2.concept.UmlsJd= bcConceptFactory.<init>(UmlsJdbcConceptFactory.java:30)

   &nbs= p;    at sun.reflect.NativeConstructorAccessorImpl.newInstan= ce0(Native Method)

   &nbs= p;    at sun.reflect.NativeConstructorAccessorImpl.newInstan= ce(Unknown Source)

   &nbs= p;    at sun.reflect.DelegatingConstructorAccessorImpl.newIn= stance(Unknown Source)

   &nbs= p;    at java.lang.reflect.Constructor.newInstance(Unknown S= ource)

 

 

Please find attached &= #8220;umls2015aa.xml” file generated by dictionary_gui tool. Why Im g= etting the above mentioned error.. Any ideas/suggestions will be helpful.

 

Thanks= &Regards

Stuti = Awasthi

&= nbsp;

From: Stuti Awasthi
Sent: Thursday, March 31, 2016 5:17 PM
To: user@ctakes.apache.org=
Subject: RE: Integrate cTakes with latest UMLS DB<= /p>

 

Thanks.

Ya I have read the long conversation bet= ween you and Sean on how to use dictionary tool utility and that really hel= ped. Thanks to Sean.

Thanks for java 8 pointer. Presently Im = using Java7 and already added libraries in build path. Let me try with Java= 8 and Il come back. 

 

Example of error : org= .apache.ctakes.dictionary.creator.gui.umls.Concept.java

concept.getTuis().stream().forEach( this::addTui );<= /span>

The method stream() is undefined f= or the type Collection<Tui>

 

This is just an example, similarly Im ge= tting more errors in different classes.

 

Thanks

Stuti Awasthi

 

From:<= /span> Geise, Brandon D. [bdgeise@geisinger.edu]
Sent: Thursday, March 31, 2016 5:02 PM
To: user@ctakes.apache.org=
Subject: RE: Integrate cTakes with latest UMLS DB

Hi Stuti,

 

All credit for the dic= tionary work goes to Sean Finan.  What errors are you getting?  I= ’m not aware of a precompiled jar.  I do remember that I needed = to switch to Java 8, if you aren’t already to compile the project.  You also may need to reference the lib folder or move those= jars to the project library path in order to compile.

 

Brandon

 

From: Stuti Awasthi [mailto:stutiawasthi@hcl.com]
Sent: Thursday, March 31, 2016 7:14 AM
To: 'user@ctakes.apache.org' <user@ctakes.apache.org>
Subject: RE: Integrate cTakes with latest UMLS DB<= /p>

 =

Hi All,

Sorry , I think I got confused with dict= ionary-gui and dictionary-tool projects. Jessica mentioned about dictionary= tool and its README which I followed along with the previous mail threads to generate umls dictionary in file format. Im s= till to use this dictionary with cTakes so i might comeback with issues.

 

Also I would like to use dictionary-gui = posted by Brandon. When I have checkout the code and imported in eclipse, i= ts showing compilation error in classes due to which even I have created the jar of the project, it is not running. Any i= dea about the compilation errors or if there is a pre built binary which ca= n be used (similar to dictionary tools jar) that would be great.

 

Thanks for your help and patience.

 

Regards

Stuti Awasthi

From:<= /span> Stuti Awasthi
Sent: Thursday, March 31, 2016 11:58 AM
To: 'user@ctakes.apache.org'
Subject: RE: Integrate cTakes with latest UMLS DB

Hi Brandon, Jessica

 

I lookedup at dictiona= ry-gui utility.  Here is what I did : Checkout the source code https://svn.apache.org/repos/asf/ctakes/sandbox/dictionary-gui/ and imp= orted in my eclipse IDE. Now I was not able to find any README with this pr= oject. Hence I checked the code and found that “CreaterGui.java”= ; might be the mail class to launch the GUI. My queries are :

· &nbs= p;       Is there any README as Jessica mention= ed or simply launching the CreaterGui.java class would be suffice.

· &nbs= p;       Is there any commands to execute tool = on linux server (without gnome) . Something like command like options? Im a= sking this because Im working on linux machine where I have installed lated= UMLS2015.

 

Few more questions:

· &nbs= p;       As Brandon mentioned : that I might ne= ed to create the tables that will have same information (based on rare /fir= st word approach). Do we know how to create those tables ?? Any SQL stateme= nts or links will be useful.<= /span>

· &nbs= p;       I found the following link in Ctakes3.= 1 documentation but looks like broken. Any clue on redirected path/links

    • <= a href=3D"https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=3D28&am= p;t=3D423" target=3D"_blank">https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=3D28&t= =3D423
    • <= a href=3D"https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=3D28&am= p;t=3D80&start=3D20#p1459" target=3D"_blank">https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopi= c.php?f=3D28&t=3D80&start=3D20#p1459
  • Can I create full dictionary(not only the fast one) from dictionary tool.

Thanks &Regards

Stuti Awasthi

 

From: Stuti Aw= asthi
Sent: Tuesday, March 29, 2016 5:35 PM
To: 'user@ctakes.apache.org'
Subject: RE: Integrate cTakes with latest UMLS DB

 =

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. [mailt= o: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 Windows 10

 

From: Stuti Awasthi
Sent: Tuesday, March 29, 2016 7:59 AM
To: 'use= r@ctakes.apache.org'
Subject: RE: Integrate cTakes with latest UMLS DB<= /p>

 

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@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 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://cta= kes.markmail.org/search/<= /span>

 

Regards,

Jessica

 

From: Stuti Aw= asthi [mailto:stu= tiawasthi@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 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 cT= akes and wanted to use latest UMLS 2015ab with it. To achieve the same, I h= ave installed UMLS in mysql database.

 =

Database Name: umls=

Numbers of Tables create= d : 53

Eg : mysql> show tabl= es;

+-------------------= -------+

| Tables_in_umls &n= bsp;         |

+-------------------= -------+

| AMBIGLUI  &n= bsp;            = ;  |

| AMBIGSUI  &n= bsp;            = ;  |

| DELETEDCUI  =              |<= o:p>

| DELETEDLUI  =              |<= o:p>

| DELETEDSUI  =

……

| SRSTRE1  &nb= sp;            =    |

| SRSTRE2  &nb= sp;            =    |

 =

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 DictionaryLo= okupAnnotatorDB.xml with jdbc url of my database along with username and pa= ssword.

 =

Now I believe I also nee= d to modify LookupDesc_DB.xml with some umls tablename which can get cui, t= ui 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 s= teps guide/document of available for cTakes integration with UMLS.

 =

Thanks &Regards=

Stuti Awasthi=

 =



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