Andrea,
I am cross-posting this to public-semweb-lifesci, since I recall this
discussion (parts of it) coming up a few times here...
-Eric
--- Andrea Splendiani <[EMAIL PROTECTED]> wrote:
This may be slightly off-topic for the biopax mailing list, but this
is probably the best list (for its audioence) where to post this.
Some questions on BioZen (I didn't have much time to review it
deeply, so some of them may be trivial):
*) From your work on BioZen, how problematic do you see the mapping
of BioPAX on an upper ontology like DOLCE ? At least for some core
parts, this what BioZen has done (I mean, among other things). Did
you find problems in this ?
*) You say that the abstract class is used for uncomplicated
representation of spatio-temporal-particulars. I see only concepts in
the ontology. Where can I find is some examples of this ? (Ok, I'm
having a look at the rattus export only)
*) In population of molecules, dol:part seems to refer both to part-
of populations (meaning: subsets of individuals of the populations)
and to part-of individuals population-wide (part of each molecule
across the whole population). To me, these two cases seems to be
associated to two different semantics, expecially if I think how
qualities of a populations affects its parts. But I'm sure this is
already covered in the DOLCE framework. Can you elaborate more on this
?
*) If I understand it well (but maybe I don't), a molecular
population is characterized by it's location. What if I want to refer
to a molecule population, independently of its location ?
*) <described-by> concept, isn't this too loose semantically ? Ok, I
understand the reasons to keep it simple. But I can say insulin123
described-by insulin and something like diabetes described-by insulin
(ok, this is a little but stretched, but... it's anyway described-by
if this not more specified). Do you think described-by may be further
specified (for example: "characterized by", "annotated by"...) ?
*) Where do you need Correlates-A,B... ? And by the way, I guess this
is to state some correspondence with a semantics implicitely encoded
in the uri-string. If so, isn't this a little dirty ? Anyway, can you
provide an example of a description of correlation that uses these
properties ?
*) Quick dumb question: does causation implies a relation in time ?
*) on fuzzness. What do you mean by realness ?
Like in: John is a thief with belief 0.7 (He is or he is not a thief,
holds)
Or
John is old with belief 0.7 (I know exactly the age, it's the concept
of old that's vague).
*) As for fuzziness, as well as evolution of description models, this
should be in some underlying level, with provenance, trust,
versioning, dependencies and so on... or not ?
These are just questions, the work is great!
best,
Andrea
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Eric Neumann, PhD
co-chair, W3C Healthcare and Life Sciences,
and Senior Director Product Strategy
Teranode Corporation
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