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From vijay garla <vnga...@gmail.com>
Subject Re: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup
Date Fri, 22 Aug 2014 03:06:36 GMT
That would definitely make sense

On Thursday, August 21, 2014, Chen, Pei <Pei.Chen@childrens.harvard.edu>
wrote:

> VJ,
> Would it make sense to add in('SNOMEDCT_US') to the default
> ctakes-ytex/scripts/data/**/insert_view.sql?
> That way it'll support umls2011 as well as the newer 2014 naming
> conventions?
> Ex: inner join MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( 'SNOMEDCT',
> 'SNOMEDCT_US','RXNORM')
>
> --Pei
>
> > -----Original Message-----
> > From: clayclay911@gmail.com <javascript:;> [mailto:clayclay911@gmail.com
> <javascript:;>] On Behalf Of
> > Clayton Turner
> > Sent: Thursday, August 21, 2014 4:25 PM
> > To: dev@ctakes.apache.org <javascript:;>
> > Subject: Re: Change from SNOMEDCT to SNOMEDCT_US affecting
> > v_snomed_fword_lookup
> >
> > Ah, I just switched to the ytex branch and all is good now. The SNOMED_US
> > issue has been plaguing me for weeks now so thanks a million for that.
> >
> >
> > On Thu, Aug 21, 2014 at 2:13 PM, Clayton Turner <caturner3@g.cofc.edu
> <javascript:;>>
> > wrote:
> >
> > > Awesome. This is just what I needed for the longest time.
> > >
> > > I'm having a slight issue. When running either the ytex pipeline or
> > > ytex version of the AggregatePlaintextUMLSProcessor I get an error
> > > during initialization.
> > >
> > > My DictionaryLookupAnnotator.xml is raising a
> > > org.apache.uima.resource.ResourceInitializationException causedby:
> > > java.lang.ClassNotFoundException:
> > > edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
> > >
> > > I feel like I may have drifted away from what I need, though, because
> > > before this the CPE was complaining about a lack of
> > > LookupDesc_SNOMED.xml file. I found a ytex version of this on a google
> > > code site somewhere and pasted it where the CPE was looking for it. Now
> > this error is coming up.
> > >
> > > Could my problem be solved with just a re-run of the ant script (was
> > > just trying to avoid since it takes ages) or is it a different issue?
> > >
> > >
> > > On Tue, Aug 19, 2014 at 12:58 PM, Tim O'Connell
> > > <tim.oconnell@gmail.com <javascript:;>>
> > > wrote:
> > >
> > >> 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 <javascript:;>>
> > >> 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 <javascript:;>>
> > >> > 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_templ
> > >> ate.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
> > >> >
> > >>
> > >
> > >
> > >
> > > --
> > > --
> > > Clayton Turner
> > > email: caturner3@g.cofc.edu <javascript:;>
> > > phone: (843)-424-3784
> > > web: claytonturner.blogspot.com
> > >
> > > ----------------------------------------------------------------------
> > > --------------------------- “When scientifically investigating the
> > > natural world, the only thing worse than a blind believer is a seeing
> > > denier.”
> > > - Neil deGrasse Tyson
> > >
> >
> >
> >
> > --
> > --
> > Clayton Turner
> > email: caturner3@g.cofc.edu <javascript:;>
> > phone: (843)-424-3784
> > web: claytonturner.blogspot.com
> >
> ----------------------------------------------------------------------------------------------
> > ---
> > “When scientifically investigating the natural world, the only thing
> worse than
> > a blind believer is a seeing denier.”
> > - Neil deGrasse Tyson
>

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