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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup
Date Thu, 21 Aug 2014 20:45:48 GMT
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 [mailto:clayclay911@gmail.com] On Behalf Of
> Clayton Turner
> Sent: Thursday, August 21, 2014 4:25 PM
> To: dev@ctakes.apache.org
> 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>
> 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>
> > 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>
> >> 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_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
> > 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
> 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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