Re: [BioPAX-discuss] Again about BioZen

From: Eric Neumann <eneumann@teranode.com> · Date: Fri, 13 Oct 2006 17:19:25 -0400

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 <andrea@pasteur.fr> 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
411 1st Avenue South, Suite 700
Seattle, WA 98104
+1 (781)856-9132
www.teranode.com 