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From Erin Nicole Gustafson <erin.gustaf...@northwestern.edu>
Subject RE: UMLS version in dictionary-gui
Date Thu, 09 Feb 2017 17:45:21 GMT
Yes and yes. Just for my own understanding, why would it be the case that certain custom dictionaries
from the GUI (T047 only) run fine but others with more TUIs don't?

Is there any way to still use the custom dictionary in 3.2.2 by modifying the configuration
file to make it compatible?

-Erin

-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu] 
Sent: Thursday, February 09, 2017 11:25 AM
To: dev@ctakes.apache.org
Subject: RE: UMLS version in dictionary-gui

Hi Erin,

Are you using the dictionary gui and ctakes 3.2.2 ?  The dictionary gui creates a database
usable by 3.2.3 (trunk).  There are improvements in the dictionary-lookup-fast module that
use a slightly different database configuration file.

Sean

-----Original Message-----
From: Erin Nicole Gustafson [mailto:erin.gustafson@northwestern.edu] 
Sent: Thursday, February 09, 2017 12:21 PM
To: dev@ctakes.apache.org
Subject: RE: UMLS version in dictionary-gui

Hi Sean,

Ah well I discovered that I had installed UMLS incorrectly. I rectified that error and now
have the single mrconso file as expected. However, I'm still getting the same error I was
originally receiving when trying to use my custom dictionary in the cTAKES clinical pipeline:

09 Feb 2017 11:16:01  INFO JdbcConnectionFactory -  Database connected
09 Feb 2017 11:16:01 ERROR JdbcConceptFactory - Could not create Concept Data Selection Call
java.sql.SQLException: Table not found in statement [SELECT * FROM long WHERE CUI = ?] etc.

I've tested the tool by making a custom dictionary with just T047 and it runs no problem.
It must be some problem with the TUIs I'm adding that differ from the defaults selected in
the tool? Any thoughts?

Thanks,
Erin


-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu] 
Sent: Wednesday, February 08, 2017 3:34 PM
To: dev@ctakes.apache.org
Subject: RE: UMLS version in dictionary-gui

Hi Erin,

Where did you get that copy of the umls?  I have 2016AA and it has the standard .rrf filenames.

As long as your .aa/.ab files have the standard mrconso.rrf format, you should be able to
rename them to mrconso.rrf.

Sean

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_books_NBK9685_&d=CwIFAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Dgs2SzWIrHv8-_z6aTQMb9T-HW5-XqFcYRtqzvjdZSU&m=nXi0dQSmFhs1U1AmEw9pMduDTUhBXx_zxT-XKLuyUlQ&s=JR2wEJRF-J3wPXWl-07Ylyk3aDdBuwd8EkQ7hkDQ5yM&e=


-----Original Message-----
From: Erin Nicole Gustafson [mailto:erin.gustafson@northwestern.edu] 
Sent: Wednesday, February 08, 2017 4:29 PM
To: dev@ctakes.apache.org
Subject: UMLS version in dictionary-gui

Hello,

Is there a particular version of the UMLS that must be used when creating custom dictionaries
using the dictionary GUI tool? I ask because the more recent versions of the UMLS include
two MRCONSO files (.aa and .ab), which is not compatible with the current implementation of
the GUI tool. Is it best to just use an older version of the UMLS (if so, which version) or
has anyone had success modifying the source code to use both files in newer versions?

Thanks,
Erin

----
Erin Gustafson
Post-doctoral Fellow, Center for Health Information Partnerships Feinberg School of Medicine,
Northwestern University


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