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: clayclay...@gmail.com [mailto:clayclay...@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 <caturn...@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.oconn...@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.gr...@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.oconn...@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: caturn...@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: caturn...@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