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From Harpreet Khanduja <hsk5...@rit.edu>
Subject Re: v_snomed_fword_lookup view
Date Mon, 11 Aug 2014 17:04:59 GMT
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\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 <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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