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:[email protected]] > Sent: Thursday, August 21, 2014 11:07 PM > To: [email protected] > 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 <[email protected]> > 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: [email protected] <javascript:;> > > > [mailto:[email protected] > > <javascript:;>] On Behalf Of > > > Clayton Turner > > > Sent: Thursday, August 21, 2014 4:25 PM > > > To: [email protected] <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 > > > <[email protected] > > <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 > > > > <[email protected] <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 > > > >> <[email protected] <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 > > > >> > <[email protected] <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: [email protected] <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: [email protected] <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 > >
