I have not had time to implement this - to clarify out of curiosity, does this clear up the @db.schema@ error Tim? And did you successfully run ytex with the ctakes dictionary-lookup?
JG — Sent from Mailbox for iPhone On Sat, Aug 16, 2014 at 2:53 AM, Tim O'Connell <tim.oconn...@gmail.com> wrote: > Hi folks, > I was having an issue with the current build (from svn) of ctakes/ytex not > identifying any annotations as some folks on this board. I traced it to > the fact that the UMLS database has at sometime in the relatively recent > past changed the SAB tag in the MRCONSO table for SNOMED terms from > SNOMEDCT to SNOMEDCT_US. I just had a newer version of UMLS that uses > SNOMEDCT_US. Thus when the install script tried to create the > v_snomed_fword_lookup table, it wasn't finding any of the SNOMEDCT terms, > thus nothing was getting annotated. > The ytex install script was just looking for things in MRCONSO with the > SNOMEDCT SAB tag when it created the ytex lookup table - so, by changing > this to SNOMEDCT_US in the file > CTAKES_HOME/bin/ctakes-ytex/scripts/data/mysql/umls/insert_view_template.sql > it now works (for mysql users) to find the annotations. You can just re-run > the ytex setup script, but that takes hours - instead, I just deleted all > the data from the v_snomed_fword_lookup table and basically ran the sql > command to repopulate the table and it worked fine. Here's the code, n.b. > my schema name for my umls database is 'umls' - change the code below if > yours is different. > delete from v_snomed_fword_lookup; > insert into v_snomed_fword_lookup (cui, tui, fword, fstem, tok_str, > stem_str) > select mrc.cui, t.tui, c.fword, c.fstem, c.tok_str, c.stem_str > from umls_aui_fword c > inner join umls.MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( > 'SNOMEDCT_US', 'RXNORM') > inner join > ( > select cui, min(tui) tui > from umls.MRSTY sty > where sty.tui in > ( > 'T019', 'T020', 'T037', 'T046', 'T047', 'T048', 'T049', 'T050', > 'T190', 'T191', 'T033', > 'T184', > 'T017', 'T029', 'T023', 'T030', 'T031', 'T022', 'T025', 'T026', > 'T018', 'T021', 'T024', > 'T116', 'T195', 'T123', 'T122', 'T118', 'T103', 'T120', 'T104', > 'T200', 'T111', 'T196', 'T126', 'T131', 'T125', 'T129', 'T130', > 'T197', 'T119', 'T124', 'T114', 'T109', 'T115', 'T121', 'T192', > 'T110', 'T127', > 'T060', 'T065', 'T058', 'T059', 'T063', 'T062', 'T061', > 'T074', 'T075', > 'T059' > ) > group by cui > ) t on t.cui = mrc.cui > ; > Hope it helps - cheers, > Tim
