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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 18:13:38 GMT
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

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