Thanks Harpreet, That is definitely necessary to build! Those lines should already be in the pom, but commented out. I think that some version/branching issues may have arisen at some point wrt this module ...
If somebody beats me to it then cheers, otherwise I will try to check out tonight and get all the bits in place. Sean > -----Original Message----- > From: Harpreet Khanduja [mailto:hsk5...@rit.edu] > Sent: Monday, August 11, 2014 1:12 PM > To: dev@ctakes.apache.org > Subject: Re: v_snomed_fword_lookup view > > 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\cTake > > sSnomed.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 > >