>Ingvar,
>
>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. (01)
There isn't going to be a SINGLE philosophical
way of looking at almost any picture. I would
suggest looking at how actual formal ontologies
do this. Good places to start would be the CYC
on-line documentation and Matthew West's work.
Cyc for example has descriptions of the Krebs
cycle, which use its spatiotemporal concepts
(which are an ad-hoc mixture of what people call
4-d and 3-d modes of description; the CYC
reasoner can translate between these robustly,
but you might want to fix on one of the basic
styles for simplicity.) (02)
What formal language is your ontology being
written in? I ask because if you are using OWL or
something similar, many of the subtler
distinctions will not be expressible in any case. (03)
Pat Hayes (04)
>
>regards,
>erick
>
>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
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>
>--
>==================================================================
>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
>==================================================================
>
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