I still get the same error with the ctakes3.2 branch. Any suggestions?
On Mon, Aug 11, 2014 at 12:06 PM, Clayton Turner <caturn...@g.cofc.edu> wrote: > I'm going to do a clean install through the repo rather than the binaries > and see if that fixes my issue because I think I just read a past post > saying the lookup2 folders exist there. > > > On Mon, Aug 11, 2014 at 11:52 AM, Clayton Turner <caturn...@g.cofc.edu> > wrote: > >> When navigating to ctakes-dictionary-lookup-fast\desc\analysis_engine >> there are 2 files, assumedly analysis engines. >> >> SnomedLookupAnnotator.xml and SnomedOvLookupAnnotator.xml >> >> If I pick either, I put in my UMLS information but receive an error when >> trying to run the CPE: >> >> Initialization of CAS Processor with name "SnomedOvLookupAnnotator" >> failed. >> CausedBy: org.apache.uima.resource.ResourceConfigurationException: >> Initialization of CAS processor with name "SnomedOvLookupAnnotator" >> failed. >> CausedBy: org.apache.uima.resource.ResourceInitializationException: Error >> initializing "org.apache.uima.resource.impl.DataResource_impl" from >> descriptor >> file:..............SnomedLookupAnnotator.xml >> CausedBy: org.apache.uima.resource.ResourceInitializationException: Could >> not >> access the resource data at >> >> file:org\apache\ctakes\dictionary\lookup2\Snomed2011ab_ctakesTui\cTakesSnomed.xml >> >> Now, I don't even have a "lookup2" folder and, subsequently the Tui >> folder and cTakesSnomed.xml file. This seems to be the problem, but I'm not >> sure where these files are supposed to be grabbed from. >> >> >> On Mon, Aug 11, 2014 at 11:47 AM, Clayton Turner <caturn...@g.cofc.edu> >> wrote: >> >>> Hi again: >>> >>> How exactly do you switch to using the cTakes dictionary-lookup-fast. Do >>> I need to go in and alter xml files or is it as simple as adding a certain >>> item to the list of analysis engines? >>> >>> >>> On Fri, Aug 8, 2014 at 3:48 PM, Finan, Sean < >>> sean.fi...@childrens.harvard.edu> wrote: >>> >>>> Hi Clayton, >>>> >>>> I don't know how the ytex dictionary lookup works, so I'm afraid that I >>>> can't help you with an answer. Maybe Vijay is the best person to do this. >>>> If you aren't tied to ytex you could try the new cTakes >>>> dictionary-lookup-fast. I tested "Patient came in with a malar rash" and >>>> it found "malar" and "malar rash". >>>> >>>> Vijay, >>>> >>>> At some point the lookup-fast module will be the default for the cTakes >>>> clinical pipeline. In order to synchronize the ytex lookup with cTakes, >>>> would you like to eventually work together on reusing the same code for >>>> ytex? I have no idea what ytex does, but I know the ins and outs of the >>>> cdl-fast module. >>>> >>>> Sean >>>> >>>> > -----Original Message----- >>>> > From: clayclay...@gmail.com [mailto:clayclay...@gmail.com] On Behalf >>>> Of >>>> > Clayton Turner >>>> > Sent: Friday, August 08, 2014 2:08 PM >>>> > To: dev@ctakes.apache.org >>>> > Subject: v_snomed_fword_lookup view >>>> > >>>> > Hi Everyone: >>>> > >>>> > I have a question about how the v_snomed_fword_lookup view works when >>>> > running the CPE. >>>> > >>>> > So my understanding of the view is that it is a view comprised of the >>>> > ytex.umls_aui_fword table, the umls.mrconso table and bits/pieces from >>>> > other umls tables. >>>> > >>>> > I feel like this is not completely correct or my idea of how the join >>>> to >>>> > create the view works is off. For example, let's say I want the CPE >>>> to find >>>> > "malar ____" (e.g. malar rash) as a concept in the annotations. It >>>> never >>>> > happens after running my CPE descriptor and I cannot find it in my >>>> > v_snomed_fword_lookup view. >>>> > >>>> > select count(*) from umls_aui_fword where fword='malar'; yields 34 >>>> results >>>> > >>>> > select count(*) from umls.mrconso where str='malar'; yields 3 results. >>>> > >>>> > So clearly these two tables know what the cui and context(s) are for >>>> malar >>>> > ____. Yet, whenever I run a gold standard set of notes through the >>>> CPE, >>>> > malar is constantly flagged as just a word token and the concept is >>>> never >>>> > grabbed. This is recurrent for lots of other concepts, as well, I just >>>> > wanted to use an example to illustrate my issue. >>>> > >>>> > Some troubleshooting I already went through: >>>> > 1) Reinstalled ytex and umls database objects >>>> > 2) Reinstalled a second time after redownloading umls through >>>> > metamorphosys, ensuring that snomed vocabularies were included (also >>>> > checked file sizes and noticed a big difference so I know those >>>> > vocabularies ARE included >>>> > >>>> > Anyone got any ideas as to what the issue could be? >>>> > >>>> > Thank you, >>>> > Clayton Turner >>>> >>> >>> >>> >>> -- >>> -- >>> 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 >> > > > > -- > -- > 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
