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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 Tue, 19 Aug 2014 16:58:20 GMT
Hi John,

I'm not sure what was going on with the @db.schema@ error, although I was
getting it as well before with my prior build of 3.1.2 - I assume that
you've fixed something (thank you!) to make this go away.  I rebuilt
everything from scratch and it's working now.

I think one other thing I had to change was that after I had finished the
install/build, the cTakes version of LookupDesc_Db.xml doesn't work (in
resources\org\apache\ctakes\dictionary\lookup) - I'm pretty sure I had to
copy in an older version of the file from 3.1.1 to get the default cTakes
AggregatePlaintextUMLSProcessor pipeline working, although please
double-check that as my memory is a little foggy.

But yes, here's what I have working since re-building:
1. ytex-pipeline.xml
2. ytex version of AggregatePlaintextUMLSProcessor.xml
3. cTakes version of AggregatePlaintextUMLSProcessor.xml (with swapping the
LookupDesc_Db.xml file as above)

I've even made modifications to the ytex version of LookupDesc_SNOMED.xml
to get it tagging Disease Disorders, along with database modifications to
have it store these entries as well, which is working great.   Literally,
everything is working perfectly now.

Still so much for me to learn!  Let me know if you need any more details.

All the best,
Tim



On Tue, Aug 19, 2014 at 4:31 AM, John Green <john.travis.green@gmail.com>
wrote:

> 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.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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