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Re: [ontolog-forum] Confusion about 'model'

To: "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>, "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "Smith, Barry" <phismith@xxxxxxxxxxx>
Date: Sun, 15 Jul 2007 22:46:15 +0200
Message-id: <20070715210236.655FC109C38@xxxxxxxxxxxxxxxxx>
At 04:39 PM 7/15/2007, Gary Berg-Cross wrote:
>Barry asked:
> >But when one is building an ontology for, e.g., cell biology, is one
> >trying to build a model of the cell, or rather to create a formally
> >coherent controlled vocabulary for talking about cells and their parts?    (01)

Gary Berg-Cross responded:
>I would say that we have 3 subjects here.
>There is the cell in reality.  There are what are called 
>biological  models of a cell that have been developed as part of 
>that science and there is now an attempt an ontological "model" of the cell.
>Of course, to be any good we should leverage the biological model to 
>guide us in what the  "coherent, controlled vocabulary" (and 
>constraints) of the ontological model will express. So we are not 
>trying to build a cell model from scrathc  but we are using a model 
>and adapting it to ontological purposes.  In the process we may 
>simplify the biological model to reflect expressivity constraints 
>etc.  So in the end we may indeed have a model, but at this stage of 
>ontological engineering probably not as good as the biological 
>one.  Of course in the process of formalizing things we may discover 
>some inaccuracies in the way the biological model expressed some things.    (02)

This has certain uncomfortable consequences. E.g.:    (03)

If we have a sentence in a biology textbook, say 'blood cells are 
non-nucleated', then is this about cells in reality (as I, and I 
guess common sense, would assume) or about cells in the biology model?    (04)

BS    (05)

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