Yes, absolutely and no problem at all. Regards, Harpreet
On Mon, Aug 11, 2014 at 1:16 PM, Finan, Sean < [email protected]> wrote: > 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:[email protected]] > > Sent: Monday, August 11, 2014 1:12 PM > > To: [email protected] > > 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 <[email protected]> > > 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 > > > <[email protected]> > > > 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 > > > > <[email protected]> > > > > 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 > > > >> <[email protected]> > > > >> 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 < > > > >>> [email protected]> 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: [email protected] [mailto:[email protected]] On > > > Behalf > > > >>>> Of > > > >>>> > Clayton Turner > > > >>>> > Sent: Friday, August 08, 2014 2:08 PM > > > >>>> > To: [email protected] > > > >>>> > 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: [email protected] > > > >>> 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: [email protected] > > > >> 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: [email protected] > > > > 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: [email protected] > > > 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 > > > >
