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From Clayton Turner <caturn...@g.cofc.edu>
Subject Re: v_snomed_fword_lookup view
Date Mon, 11 Aug 2014 16:06:27 GMT
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

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