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
