Hi Brandon, Jessica
I lookedup at dictionary-gui utility. Here is what I did : Checkout the source
code https://svn.apache.org/repos/asf/ctakes/sandbox/dictionary-gui/ and
imported in my eclipse IDE. Now I was not able to find any README with this
project. Hence I checked the code and found that "CreaterGui.java" might 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 gnome)
. Something like command like options? Im asking this because Im working on
linux machine where I have installed lated UMLS2015.
Few more questions:
* As Brandon mentioned : that I might need to create the tables that
will have same information (based on rare /first word approach). Do we know how
to create those tables ?? Any SQL statements or links will be useful.
* I found the following link in Ctakes3.1 documentation but looks like
broken. Any clue on redirected path/links
* https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=423
*
https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80&start=20#p1459
* Can I create full dictionary(not only the fast one) from dictionary tool.
Thanks &Regards
Stuti Awasthi
From: Stuti Awasthi
Sent: Tuesday, March 29, 2016 5:35 PM
To: '[email protected]'
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:[email protected]]
Sent: Tuesday, March 29, 2016 5:32 PM
To: Stuti Awasthi; '[email protected]'
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<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
From: Stuti Awasthi<mailto:[email protected]>
Sent: Tuesday, March 29, 2016 7:59 AM
To: '[email protected]'<mailto:[email protected]>
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!
Regards
Stuti Awasthi
From: Glover, Jessica [mailto:[email protected]]
Sent: Tuesday, March 29, 2016 5:17 PM
To: '[email protected]'
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/
Regards,
Jessica
From: Stuti Awasthi [mailto:[email protected]]
Sent: Tuesday, March 29, 2016 7:10 AM
To: '[email protected]'
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: [email protected]<mailto:[email protected]>
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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