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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.

Thanks,
Brandon


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               |
| DELETEDSUI
......
| 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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