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From Clayton Turner <caturn...@g.cofc.edu>
Subject Re: v_snomed_fword_lookup view
Date Mon, 11 Aug 2014 15:47:01 GMT
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

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