ctakes-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Geise, Brandon D." <bdge...@geisinger.edu>
Subject RE: Integrate cTakes with latest UMLS DB
Date Tue, 29 Mar 2016 11:40:26 GMT
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.


From: Stuti Awasthi [mailto:stutiawasthi@hcl.com]
Sent: Tuesday, March 29, 2016 7:10 AM
To: 'user@ctakes.apache.org' <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<mailto: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               |
| SRSTRE1                  |
| SRSTRE2                  |

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

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,
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.
View raw message