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 <caturn...@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 <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_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: 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
