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RE: Ontology Working Group Proposal Draft

From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
Date: Mon, 6 Feb 2006 07:45:07 -0800
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>
cc: "public-semweb-lifesci" <public-semweb-lifesci@w3.org>
Message-ID: <E1F68YK-00073g-D2@lisa.w3.org>

Hi Vipul and Adrian,

> However, in  order for 
> these ontological
> artifacts to be useful to practitioners, we have to adopt the
> "model of use" perspective as well.

>From my (admittedly limited) point of view, for microarray experiments,
our use case for ontologies is that we wish to attach annotation from
standardized ontologies so that what we mine are common microarray
experiments, i.e. an investigator may be working on liver cancer and is
interested in a particular cellular pathway with a set of gene
biomarkers.  this investigator would like to go out via the semantic web
and find other microarray experiments, possibly proteomic experiments
and also related literature.


> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> Kashyap, Vipul
> Sent: Sunday, February 05, 2006 9:59 AM
> To: Adrian Walker
> Cc: public-semweb-lifesci; John Madden; Vinay K. Chaudhri; 
> wangxiao@musc.edu; duncan.hull@cs.man.ac.uk; Robert Stevens; 
> Amit Sheth @ LSDIS; Alfredo Morales; Ullman-Cullere, Mollie; 
> ray.hookway@hp.com; Mark Musen
> Subject: RE: Ontology Working Group Proposal Draft
> > "The current definition of an ontology as enunciated by the 
> W3C needs to
> > be
> > examined and extended if required. Ontology as a model of 
> use needs to be
> > emphasized in contrast to ontology as a model of meaning."
> > 
> > In admittedly limited reading of the ontology literature, I 
> have formed
> > the
> > impression that "ontology as a model of meaning" is what 
> OWL is about,
> > while "ontology as a model of use" often seems to require 
> tools that are
> > built on top of OWL.
> [VK] We clearly recognize the fact that the current 
> discussions around ontology
> have adopted the "model of meaning". However, in  order for 
> these ontological
> artifacts to be useful to practitioners, we have to adopt the
> "model of use" perspective as well.
> In fact that model of use perspective is what has lead to 
> development of
> vocabularies, database schemas, terminologies, etc. We have 
> to "assimilate and
> extend"
> It may be noted that the two perspectives are likely to 
> overlap to a large
> extent. Now whether we need to extend the current RDF, OWL, 
> SWRL standards to
> accommodate this perspective or come up with tools, 
> techniques and best
> practices based on the current standards is for the group as 
> a whole to explore.
> > To try to ground this a bit in something that a healthcare 
> practitioner or
> > a clinical researcher
> > might in future find useful, there are some pointers below to some
> > examples
> > that one can run using a browser.
> [VK] Thanks for the examples. Will take a look and get back to you.
> Cheers,
> ---Vipul
Received on Monday, 6 February 2006 15:45:32 UTC

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