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Re: [Obo-relations] Advancing translational research with the Semantic Web (Not clear about definition of <is_location_of_process>)

From: William Bug <William.Bug@DrexelMed.edu>
Date: Thu, 31 May 2007 21:42:36 -0400
Message-Id: <450B4A30-87EA-47BB-B216-99298DA409DC@DrexelMed.edu>
Cc: "Smith, Barry" <phismith@buffalo.edu>, "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, samwald@gmx.at, public-semweb-lifesci@w3.org, obo-relations@lists.sourceforge.net
To: Kei Cheung <kei.cheung@yale.edu>
Barry beat me to the punch here -


I would not want to miss out on the specific value of the proposal  
Kei has made.

I believe looking closely at how the OBI representation of microarray- 
associated instruments, protocols, reagents, data artifacts,  
algorithms, etc. - could be put to use in describing some of the data  
being produced for the NIH Neuroscience Microarray Consortium that  
you are contributing to, Kei.  As you may already know, many of the  
experts working on FuGE (grown out of MAGE which used the MGED  
Ontology as its shared semantic framework) are looking for assistance  
in how to make use of ontologies when representing microarray data in  
a FuGE instance.  As you also probably know, the original FuGE- 
associated ontology, FuGO, has expanded its domain to cover all forms  
of biomedical investigation (Ontology of Biomedical Investigation -  
aka the OBI that Barry cited).  This was a part of the evolution of  
FuGO as it began to participate in the OBO Foundry AND make a  
commitment to use BOTH the OBO Relations ontology and BFO.

With that in mind - and considering the NIH Neuroscience Microarray  
Consortium is committed to providing array data in FuGE format - it  
could be very helpful both to understand how OBI can be used to  
provide a formal semantic representation of important experimental  
provenance information AND how SemWebTech in general could be used to  
provide a more flexible - and query-able - framework in which to  
access this semantic information.


On May 31, 2007, at 9:21 PM, Kei Cheung wrote:

> Smith, Barry wrote:
>> At 08:52 PM 5/31/2007, Kei Cheung wrote:
>>> Hi Barry,
>>> Welcome to the SWHCLS list. Such a discussion reminds me of the  
>>> Nature paper: "Are the current ontologies in biology good  
>>> ontologies?" (http://www.nature.com/nbt/journal/v23/n9/full/ 
>>> nbt0905-1095.html). The paper uses the MGED (microarray) ontology  
>>> to illustrate some of the ontological issues. I'm just curious  
>>> how the BFO principles and practice can help make such a  
>>> microarray ontology more ontologically sound and therefore more  
>>> machine readable.
>> We are already working on it:
>> http://obi.sf.net
>> BS
> That's great! I hope we can develop some real use case of it.
> -Kei

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
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, 1 June 2007 01:40:16 UTC

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