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
