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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: v_snomed_fword_lookup view
Date Mon, 11 Aug 2014 17:16:42 GMT
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:hsk5004@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 <caturner3@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
> > <caturner3@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
> > > <caturner3@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
> > >> <caturner3@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.Finan@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: clayclay911@gmail.com [mailto:clayclay911@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: caturner3@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: caturner3@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: caturner3@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: caturner3@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
> >
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