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

From: Kei Cheung <kei.cheung@yale.edu>
Date: Thu, 31 May 2007 22:05:13 -0400
To: William Bug <William.Bug@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
Message-id: <465F7ED9.6020406@yale.edu>

Hi Bill,

Thanks for describing the evolution of MGED into FuGO. As I understand 
it, the consortium's microarray data can be exported in MAGE-ML (XML) 
format. Would it be possible to convert it to the FuGE format?

Cheers,

-Kei

 William Bug wrote:

> Barry beat me to the punch here - 
>
> BUT - 
>
> 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.
>
> Cheers,
> Bill
>
> 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
> 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 
> <mailto:William.Bug@DrexelMed.edu>
>
>
>
>
Received on Friday, 1 June 2007 02:05:36 GMT

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