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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 Mon, 25 Aug 2014 21:23:02 GMT
This has been done in trunk for the next patch 3.2.1 release:
https://issues.apache.org/jira/browse/CTAKES-309
Thanks for pointing this out- Would be great if someone could confirm the ytex scripts works
as expected with their latest version of umls.


> -----Original Message-----
> From: vijay garla [mailto:vngarla@gmail.com]
> Sent: Thursday, August 21, 2014 11:07 PM
> To: dev@ctakes.apache.org
> Subject: Re: Change from SNOMEDCT to SNOMEDCT_US affecting
> v_snomed_fword_lookup
> 
> 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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