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Re: [Fwd: Re: cell types, brain regions mentioned in gensat]

From: William Bug <William.Bug@DrexelMed.edu>
Date: Fri, 2 Mar 2007 17:40:05 -0500
Message-Id: <9AEE7F03-BEF2-4A45-A2D1-79E0B527DDF8@DrexelMed.edu>
Cc: Kei Cheung <kei.cheung@yale.edu>, HCLS <public-semweb-lifesci@w3.org>
To: Alan Ruttenberg <alanruttenberg@gmail.com>
Thanks, Alan.

I'd posted a question about this statement on that Wiki page.  It  
didn't quite make sense to me but wanted to hear what it was  
originally intended to assert.

This is partly why I think its a good idea to look at the simpler,  
less expressive representation I have on the followup page.  I think  
it will be easier for us to apply to the current data sets we have in  
hand and to scale up.
	http://esw.w3.org/topic/HCLS/OntologyTaskForce/ 
OboPhenotypeSyntaxExperiment

Cheers,
Bill

On Mar 2, 2007, at 3:37 PM, Alan Ruttenberg wrote:

>
>
> On Mar 2, 2007, at 1:59 PM, Kei Cheung wrote:
>
>>
>> On that page, it describes the following OWL axiom example:
>>
>> *EquivalentClass*(CerebellarPurkinjeCell *intersectionOf* 
>> (PurkinjeNeuron, *Restriction*(locatedInBrainRegion *allValuesFrom* 
>> (Cerebellum)))
>>
>> We can use a similar axiom to define the localization of a certain  
>> type of neuron cell type (CA1 pyramidal neuron) in a particular  
>> brain region (e.g., hippocampus). Due to my limited knowledge of  
>> OWL, can this type of axioms/rules be parameterized (e.g., cell  
>> type and brain region can be treated as variables)?
>
> Not sure what you mean by parameterized here. Certainly we could,  
> from a spreadsheet encoding this information, generate the  
> appropriate classes.
>
> Also, in LSW or (dig) one can easily construct one of these classes  
> on the fly and ask what the equivalent, subclasses, and  
> superclasses are.
>
> To find all cells located in, e.g. Cerebellum you would ask for  
> subclasses of
>
> intersectionOf*(Cell, *Restriction*(locatedInBrainRegion  
> *allValuesFrom*(Cerebellum))
>
> Don't think I'd use locatedInBrainRegion though, probably just  
> locatedIn, or partOf, or perhaps derivedFrom some PartOf if the  
> cells were no longer in the brain (i.e. in a dish).
>
> -Alan
>
>

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu
Received on Friday, 2 March 2007 22:40:11 UTC

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