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Date: Sat, 16 Aug 2014 09:07:23 -0700 (PDT)
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From: "John Green" <john.travis.green@gmail.com>
To: dev@ctakes.apache.org
Cc: dev@ctakes.apache.org
Subject: Re: Change from SNOMEDCT to SNOMEDCT_US affecting
 v_snomed_fword_lookup
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Great catch!=E2=80=94
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=5FUS.  I just had a newer version of UMLS that uses
> SNOMEDCT=5FUS.  Thus when the install script tried to create the
> v=5Fsnomed=5Ffword=5Flookup 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=5FUS in the file
> CTAKES=5FHOME/bin/ctakes-ytex/scripts/data/mysql/umls/insert=5Fview=5Ftem=
plate.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=5Fsnomed=5Ffword=5Flookup 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=5Fsnomed=5Ffword=5Flookup;
> insert into v=5Fsnomed=5Ffword=5Flookup (cui, tui, fword, fstem, =
tok=5Fstr,
> stem=5Fstr)
> select mrc.cui, t.tui, c.fword, c.fstem, c.tok=5Fstr, c.stem=5Fstr
> from umls=5Faui=5Ffword c
> inner join umls.MRCONSO mrc on c.aui =3D mrc.aui and mrc.SAB in (
> 'SNOMEDCT=5FUS', '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 =3D mrc.cui
> ;
> Hope it helps - cheers,
> Tim
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