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From Stuti Awasthi <stutiawas...@hcl.com>
Subject RE: Integrate cTakes with latest UMLS DB
Date Tue, 29 Mar 2016 12:05:23 GMT
Thanks Brandon, then I will check dictionary-gui tool and try to use it and will get back with
queries if any.

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.


Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

From: Stuti Awasthi<mailto:stutiawasthi@hcl.com>
Sent: Tuesday, March 29, 2016 7:59 AM
To: 'user@ctakes.apache.org'<mailto:user@ctakes.apache.org>
Subject: RE: Integrate cTakes with latest UMLS DB

Thanks Brandon, Jessica for response. I will look at dictionary tools as mentioned and will
try to figure out how it can be used for my purpose. I will certainly get back on mailing
list with more queries if any.

As of now with limited understanding, I understand that current UMLS2015 database will be
converted to hsql format which I can use in the pipeline by changing configurations in required
XMLs.  One more query, cTakes also provides "DictionaryLookupAnnotatorDB" which is supposed
to be used if we want to connect to required tables in umls database. 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 included in dictionary lookup.

Thanks for the help!

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. However, 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/


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<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

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