Tom and Azamat, (01)
I realize that a lot of hard work has gone into writing that
document, but some of it raises more questions than it can
answer. In particular, words like 'conceptualization' and
'representation' are especially frustrating, because they
are used in conflicting ways that create more confusion
than enlightenment. (02)
TG> The draft document is written as a logical walk down
> a set of distinctions, so that we could discuss the source
> of disagreements and clearly identify the point of departure. (03)
That opening section was not clear at all. And as I said,
there is no "point of departure" between philosophy and
computer science when it comes to ontology. (04)
TG> To say there is no difference between what a professor
> of Aristotelian ontology means by ontology and what a
> bioinformatics computer scientist managing a gene database
> means is absurd. (05)
No. If they both have a good background in logic, they
would be in complete agreement about the definition of
ontology and its application to bioinfomatics. (06)
Aristotle, by the way, was a pioneer in both formal logic
*and* biology. As a result of applying his methods of
analysis, he was the first to recognize that a sponge is
an animal, not a plant. Among the experiments that he and
his students carried out was the study of how an embryo
develops: they started with 30 chicken eggs and broke
open one egg each day to examine the embryo. Biologists
recognize that as one of the first and best illustrations
of good experimental procedure. (07)
TG> There is a new word sense for ontology... (08)
No. In both philosophy and computer science, there are two
ways of using the word 'ontology'. I suggest the following
two definitions, which apply equally well to both fields: (09)
Ontology: The analysis and classification of what exists. (010)
An ontology: The result of an ontological analysis of some
domain, presented as a formal description and classification
of the types of entities and relations in that domain. (011)
These definitions apply to Aristotle's work and to "a
bioinformatics computer scientist managing a gene database." (012)
AA> I suggest to find a way and consider a kind of definition
> not isolating computing ontology from the mainstream as
> something odd and extraordinary, out of the blue sky. It is
> plain that there are fundamental ontology, a universal account
> of reality, and applied ontologies, where the computing
> ontology belongs in. (013)
I agree. (014)
AA> Computing ontology is a formal representation of reality
> and its domains, levels, and complex entities and is used to
> formulate computable models, causal algorithms, and reasoning
> strategies about the world, its parts and aspects. (015)
The last two lines of this definition apply "an ontology" as
defined above to computer systems. Therefore, I believe that
we should state a general definition (as above) and add a few
lines such as these to adapt it computer science. (016)
John (017)
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