Ingvar, (01)
thank you very much for the articles you pointed out, they are really
interesting. regarding the one about the layered mereotopology theory.
Actually, we had similar ideas for tackling the granularity issues by
defining abstraction levels (~ layers). I also think that those ideas
could also be used while dealing with "ontology partitions", so that
users interested in particular and coherent? parts of an ontology (by
the way, is there a proper name for such a (sub)ontology? and/or any
attempts for formalizing its structure?) could easily work with them
for querying for instance. (02)
Pat, (03)
yes, we are using OWL in CCO (Cell Cycle Ontology). I will take a
closer look at CYC and Matthew's work on this. (04)
regards, and thanks again.
Erick (05)
On Mar 20, 2007, at 4:21 PM, Pat Hayes wrote: (06)
>> 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.
>
> 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.)
>
> 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.
>
> Pat Hayes
>
>>
>> regards,
>> erick
>> (07)
>> Erick,
>> Now I think I understand you, and even why you used the expression
>> 'time/space is physical'. In what is traditionally called the
>> philosopphy of space and time (which I first thought of), you will
>> probaly not find anything of interest for you. Here one is concerned
>> with the nature of the utmost space and time in which everything
>> spatiotemporal is assumed to exist. But you are (I take it now)
>> looking
>> for a 'space' or spatial structure that is to cell theory what the
>> skeleton is to anatomy. In my opinion, such a 'space' is not like the
>> utmost space a *particular*; it is like properties/qualities and
>> natural
>> kinds a *universal*. That is, such a 'space' can exist at many
>> places/regions simultaneously, and it might well be called a
>> 'qualitative space'. Similar remarks can be worked out for
>> 'qualitative
>> time'.
>> Perhaps you can benefit from things done under the title 'spatial
>> reasoning', but I am not in general familiar with these things. Here,
>> though, you get links to two papers that discuss formal features of
>> the
>> kind of 'spaces' you seem to be interested in: <
>> http://ontology.buffalo.edu/geo/Layers.pdf > and
>> < http://www.acsu.buffalo.edu/~md63/RelPlApOnFin.pdf >
>> best,
>> Ingvar (08)
>>
>> 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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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
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