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
