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RE: blog: semantic dissonance in uniprot

From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
Date: Tue, 24 Mar 2009 09:23:11 -0700
Message-ID: <C9EDB84D403E654CB78E37A506E406AF022CB8A9@ussemx1101.merck.com>
To: "eric neumann" <ekneumann@gmail.com>
Cc: "W3C HCLSIG hcls" <public-semweb-lifesci@w3.org>
hi eric,
this is probably a bit naive but i can think of two examples.
one is that i often do paper examples (i'm a bit of a luddite) when i'm
working out ideas so i might sketch out some object that i will then
annotate from OWL ontologies to 'see how it works.'  this might even be
in a group environment where it is done on a white board.
another example would be someone who is going to perform a biological
experiment (perhaps gene expression) where they will jot down in their
notebook some terms from OBI to describe the type of experiment.  the
experiment doesn't work out so it is never published.
by the by, i have also found the discussion useful, i do miss bill bug's
Michael Miller 
Lead Software Developer 
Rosetta Biosoftware Business Unit 


	From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of eric neumann
	Sent: Tuesday, March 24, 2009 8:17 AM
	To: Bijan Parsia
	Cc: W3C HCLSIG hcls
	Subject: Re: blog: semantic dissonance in uniprot

	I have a (possibly) naive question, but one that comes up in the
context of a digital record/rep of the protein :

	Are OWL ontologies supposed to be applied to only digital
representations of real world things, or do some believe they actually
can be applied to the real-world things "even when no record of the
object exists in the digital space"?

	That is, if one defines a bunch of formal assertions on classes
(based on real-world evidence/experience), do these work solely on
digital KR and data forms, or do they go beyond that? I guess it may
matter whether the "digital world" is being identified with the
"conceptual world" of the mind... and that may be opening more cans of

	What I'm getting at is that if the above question is true
(ontologies only for digital forms), than the only things we can define
ontologies for are the records of things; hence why talk about explicit
record types if everything relevant is already a digital-record?  

	In addition, I also don't see references to any object being
fundamentally different to a digital record (san descriptive triples
perhaps)... can someone provide me with a counter example?


	On Tue, Mar 24, 2009 at 10:21 AM, Bijan Parsia
<bparsia@cs.man.ac.uk> wrote:

		On 24 Mar 2009, at 13:49, eric neumann wrote:

			I think this discussion has been quite useful
and important, since there are some remaining issues to be clarified by
this community. I think all points raised are good, but not equally
valid. Bijan and Phil's thoughts are very useful for me, and would
probably resonate within the informatics groups at pharma companies.
			I think a key guidance principle here is to
ensure that whatever is proposed "makes sense and works with molecular
biologists" (scientists). Perhaps existing information resources need a
major "enhancement" in order to work in a semantic web, but then let's
make it quite clear (to all possible users) what the readily perceivable
value of all these ontological adjustments will be.

		BTW, I'm perfectly happy, albeit not until summer, to do
various sorts of empirical research to help ground this discussion. I've
done surveys fo the web and user studies before. I would be interested
in knowing what sorts of questions would help people make decisions.
		In this sense I *am* all about the data :)
Received on Tuesday, 24 March 2009 16:23:57 UTC

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