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From Clayton Turner <caturn...@g.cofc.edu>
Subject Re: v_snomed_fword_lookup view
Date Mon, 11 Aug 2014 16:44:17 GMT
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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