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
