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From Clayton Turner <caturn...@g.cofc.edu>
Subject Re: v_snomed_fword_lookup view
Date Mon, 11 Aug 2014 15:52:50 GMT
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

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