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BIONT/BioRDF Telcon - 2007-02-19 follow-up - Use Case OBO Phenotype Assertion Wiki page

From: William Bug <William.Bug@DrexelMed.edu>
Date: Mon, 19 Feb 2007 14:37:31 -0500
Message-Id: <0A3F2B3F-2611-4293-B24F-D73BBA5CF38F@DrexelMed.edu>
To: public-semweb-lifesci <public-semweb-lifesci@w3.org>
Hi All,

Just a reminder that I've now done all I have time to do on this page.

Use Case OBO Phenotype Assertion Wiki page
http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology/ 
SeedOntologyDetailedFollowup#preview

I've created OBO Phenotype Assertions for the first three  
experimental observations/research statements/claims from the first  
paper listed on this page.

I again ask the more technically geeky amongst us to review this to  
determine whether this approach would appear to fit the niche I  
described in the call in reference to tying the Use Case 'free text"  
descriptions being assembled by June, Gwen, Elizabeth, Don, et. -  
providing formal assertions to back these Use Case observations to  
the BioRDF data sets and the appropriate distilled knowledge sources  
(many of which June et al. have identified in their AD/PD comparative  
Use Case table).

I would stress:
	1) This technique would be very narrowly applied to a tight set  
domain derived from the Use Case.
	2) This does not replace what is done in SWAN for the Use Cases +  
hypotheses June et al. are summarizing.  It provides a more granular,  
formal foundation for the "Claims" and "Concepts" in the SWAN model.

Finally, I include this email except from the weekend, as it helps to  
provide the larger context - outside of HCLS - for why using this  
technique is important both to HCLS and to the application of  
SemWebTech to Health Care & Life Science informatics.

Cheers,
Bill
>
>
> On Feb 17, 2007, at 12:27 PM, William Bug wrote:
>
>> Though - I would stress LTP & LTD are models of lasting, cross- 
>> synaptic physiological, morphological, & biochemical alteration.   
>> The models, per se, can functions as "distilled knowledge kernels"  
>> around which the relevant BioRDF data elements (such as the  
>> elements you cite) can be pulled together via a shared semantics.
>>
>> Part of the reason I'm pushing this PATO-based formal phenotype  
>> statement approach is:
>> 	- it uses a community-shared formal semantic framework
>> 	- it uses a formalism being shared by the community, disseminated  
>> by the NCBO, and accumulated in their "Open Biomedical Data" (OBD)  
>> repository.
>>
>> This last issue is extremely important and provides a means for  
>> whatever we produce in the demo to provide a foundation on which  
>> others can also build.
>>
>> Here are the NCBO pages describing their OBD efforts - what it is,  
>> how it fits into other community efforts, and what tools they are  
>> providing  to make productive use of this repository:
>> 	http://www.bioontology.org/obd_architecture.html
>> 	http://www.bioontology.org/repositories.html#obd
>> 	http://www.bioontology.org/wiki/index.php/OBD:SPARQL-InSitu
>> 	http://www.bioontology.org/wiki/index.php/OBD:SPARQL-GO
>>
>> You will note in the last two URLs, references to the use of  
>> SPARQL and D2RQ to create a GO annotation endpoint.  There is also  
>> a reference to the inspiration BioPAX work (OWL ED 2005 article by  
>> Joanne, Alan R, and Jonathan R - http://www.mindswap.org/ 
>> OWLWorkshop/sub37.pdf - "Experience Using OWL DL for the Exchange  
>> of Biological Pathway Information") has been to this effort - as  
>> well as an OWL ED 2006 article from Alan R, Jonathan R, & Jeremy  
>> Zucker (http://owl-workshop.man.ac.uk/acceptedLong/ 
>> submission_26.pdf - What BioPAX communicates and how to extend OWL  
>> to help it)
>>
>> I would guess at least Alan has worked with Chris Mungall (from  
>> the LBL GO/NCBO group) on this work.
>>
>> This seems to be an obvious point of contact for what we are doing  
>> in the HCLS IG (and for the demo - even given the shortness of time).
>>
>> Cheers,
>> Bill
>

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 Monday, 19 February 2007 19:37:46 GMT

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