It could be that ctakes didn't find any terms from T047, in which case it wouldn't perform any lookups in other tables. The failing sql in your email is from a secondary call that is made only after a term has been discovered.
You can modify the 3.2.3 configuration file to make it compatible with 3.2.2. You should be able to look at a 3.2.2 file and a 3.2.3 file side-by-side and see the differences. Basically a couple of names and values switched around, but nothing major. Actually, if you just point your 3.2.2 configuration file to your new database it should work just fine. Sean -----Original Message----- From: Erin Nicole Gustafson [mailto:erin.gustaf...@northwestern.edu] Sent: Thursday, February 09, 2017 12:45 PM To: dev@ctakes.apache.org Subject: RE: UMLS version in dictionary-gui 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.fi...@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.gustaf...@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.fi...@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.gustaf...@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
