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Re: [ontolog-forum] Ontological Assumptions of FOL

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Erick Antezana <erant@xxxxxxxxxxxx>
Date: Tue, 20 Mar 2007 11:25:40 +0100
Message-id: <45FFB6A4.8060001@xxxxxxxxxxxx>
Ingvar,    (01)

We are building an application ontology for the cell cycle process 
(http://www.cellcycleontology.org) in which some of the key aspects are 
indeed time and space due to the dynamic essence of this biological 
process. Actually, we are planning on "connecting" these three 
components: physical entities (= 'what') playing a role in the cell 
cycle process such as genes, proteins, etc; space (='where') entities 
such as cytoplasm, mitochondria, etc; and time (='when') entities such 
as S-phase of the cell cycle, mitosis, etc. So in that sense we are 
coming up with ways to represent it in the ontology (still under 
development). However, I was wondering whether we could get some hints 
(for dealing with spatio-temporal entities) from some articles so that 
our ontology would try to "comply with" with the philosophical (as well 
as biological) ways of looking at that picture.    (02)

erick    (03)

Ingvar Johansson wrote:
> Erick Antezana schrieb:
>> Ingvar,
>>     are there any articles or books that could be pointed out regarding 
>> those issues (time/space is physical)?
>> thanks,
>> erick
> Tell me a little more about what you are looking for, and then I will 
> come back. By the way, I didn't make the point that "time/space is 
> physical", which I happen to believe is false, even though General 
> Relativity may be taken to imply such a view (i.e., space-time is a 
> mass-energy field, and physical things are nothing else than lumps of 
> mass-energy). My point is rather that if you think a little more in tune 
> with common sense, classical physics, and molecular biology (which I 
> think is much more relevant for today's information sciences than GR) 
> then it seems natural to regard property instances as being 
> spatiotemporally located without regarding them as in themselves being 
> physical entities.
> best wishes,
> Ingvar
>> Ingvar Johansson wrote:
>>> Pat Hayes schrieb:
>>>> Well, I can see a lot of problems with this. If 
>>>> you believe, for example, that all spatiotemporal 
>>>> entities are in some sense physical, you will get 
>>>> into trouble. 
>>> Let me from my philosophical corner just add one long sentence: No 
>>> famous philosophical ontologist who posits physical (material) things in 
>>> space and time has argued that everything that exists in space and time 
>>> is physical (material); for instance, many claim that property instances 
>>> *inhere in* physical things, but this does not mean that these 
>>> spatiotemporal instances *are* physical entities.
>>> /Ingvar J
>       (04)

Erick Antezana                               Tel: 32 (0) 9 3313824
DEPARTMENT OF PLANT SYSTEMS BIOLOGY            Fax:32 (0)9 3313809
GHENT UNIVERSITY/VIB,    Technology Park 927, B-9052 Gent, Belgium
Vlaams Interuniversitair Instituut voor Biotechnologie         VIB
mailto:erant@xxxxxxxxxxxx                  http://www.psb.ugent.be
==================================================================    (05)

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