Hello Clayton, I do not know about ytex, but I did switch from dictionary-lookup to dictionary-lookup-fast. I update my ctakes-dictionary-lookup-fast project using maven. I think I used Team- Update and switched to the latest revision available and then I downloaded new 3.2 resources from the for umls. and then I added these resources to my ctakes-dictionary-lookup-fast resources folder and also the classpath in ctakes-clinical-pipeline.
Then I changed the pom.xml file which belongs to the whole ctakes project and added <dependency> <groupId>org.apache.ctakes</groupId> <artifactId>ctakes-dictionary-lookup-res</artifactId> <version>${ctakes.version}</version> </dependency> <dependency> <groupId>org.apache.ctakes</groupId> <artifactId>ctakes-dictionary-lookup-fast</artifactId> <version>${ctakes.version}</version> </dependency> these two dependencies to the file. After this, I also added the dependency <dependency> <groupId>org.apache.ctakes</groupId> <artifactId>ctakes-dictionary-lookup-fast</artifactId> </dependency> to the pom.xml of ctakes-clinical-pipeline. And then add the resources folder in ctakes-clinical-pipeline using build path configuration under "add class" option. After this it should work. Regards, Harpreet On Mon, Aug 11, 2014 at 12:44 PM, Clayton Turner <caturn...@g.cofc.edu> wrote: > 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 >