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From Clayton Turner <caturn...@g.cofc.edu>
Subject Re: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup
Date Thu, 21 Aug 2014 21:34:30 GMT
It didn't fix the @db.schema@ - I just went in and manually changed it
whenever the CPE complained. I assume that's supposed to be reading from
ytex.properties, but mine was set and it didn't resolve that @db.schema@
issue.


On Thu, Aug 21, 2014 at 5:00 PM, John Green <john.travis.green@gmail.com>
wrote:

> Clayton - this indeed did fix the @db.schema@ for you? Im gonna try and
> reproduce (havent had time yet) then ill close the Jira ticket out.
>
>
> JG
> —
> Sent from Mailbox for iPhone
>
> On Thu, Aug 21, 2014 at 1:24 PM, Clayton Turner <caturner3@g.cofc.edu>
> wrote:
>
> > 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_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
> >>> >
> >>>
> >>
> >>
> >>
> >> --
> >> --
> >> 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
>



-- 
--
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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