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From Harpreet Khanduja <hsk5...@rit.edu>
Subject Re: v_snomed_fword_lookup view
Date Mon, 11 Aug 2014 18:09:12 GMT
Yes, absolutely and
no problem at all.

Regards,
Harpreet


On Mon, Aug 11, 2014 at 1:16 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> 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: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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