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From "Tim O'Connell" <tim.oconn...@gmail.com>
Subject Re: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup
Date Sat, 16 Aug 2014 16:21:05 GMT
Thanks!

Tim


On Sat, Aug 16, 2014 at 9:07 AM, John Green <john.travis.green@gmail.com>
wrote:

> Great catch!—
> Sent from Mailbox for iPhone
>
> On Sat, Aug 16, 2014 at 2:53 AM, Tim O'Connell <tim.oconnell@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
>

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