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Re: blog: semantic dissonance in uniprot

From: eric neumann <ekneumann@gmail.com>
Date: Tue, 24 Mar 2009 11:17:19 -0400
Message-ID: <92e86c7d0903240817t672701a5q4dae90a297c41067@mail.gmail.com>
To: Bijan Parsia <bparsia@cs.man.ac.uk>
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
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

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 worms...

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 :)
> Cheers,
> Bijan.
Received on Tuesday, 24 March 2009 15:33:33 UTC

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