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
