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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: v_snomed_fword_lookup view
Date Mon, 11 Aug 2014 17:06:48 GMT
Hi Clay,
It has been a hectic day and I apologize for the late reply.

> 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.

I think that all directories "lookup2" were renamed "lookup-fast", but it looks like the links
in the xml descriptors were not updated to match.

In the SnomedLookupAnnotator.xml (or Ov equivalent), find
            <name>DictionaryDescriptorFile</name>
            <description/>
            <fileResourceSpecifier>
               <fileUrl>file:org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml</fileUrl>
            </fileResourceSpecifier>
And adjust the file url accordingly.  I haven't checked out trunk since the code was moved
(I've been busy with other things), but the equivalent file should not be difficult to find.
 Unless you are on Windows the entire path to the dictionary database must be lowercase for
hsql to work.  I think that was checked in, but if it hasn't been then you'll need to rename
the directory (and hsql files) to be all lower-case.  Also, edit the <dictionary id= ...>
line to match the rename in the cTakesSnomed.xml

If you get this working could you please check in the changes?  At some point I can do a full
checkout and do it myself, but I won't get to it for a while.

Sean

> -----Original Message-----
> From: clayclay911@gmail.com [mailto:clayclay911@gmail.com] On Behalf Of
> Clayton Turner
> Sent: Monday, August 11, 2014 11:53 AM
> To: dev@ctakes.apache.org
> Subject: Re: v_snomed_fword_lookup view
> 
> 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\cTakesSn
> omed.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
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