[MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts?

[Phillip Lord]

>>>>> "Gary" == Gary Schiltz <gss at ncgr.org> writes:

  Gary> Catherine Letondal wrote:
  >> How is the S-Moby interface defined by its "upper" ontology? I
  >> have carefully read the S-moby design document
  >> (http://www.biomoby.org/S-MOBY/doc/Design/S-MOBY_Design_Overview.html),
  >> what do you call an upper ontology there - the set of RDF graphs
  >> submitted by providers?

  Gary> Phil, since you're the ontology guy

Having just been to the semantic web conference, I've realised that
really, I'm a yeast biologist!

  Gary> feel free to chip in. If I understand the term "upper
  Gary> ontology" correctly, it refers to concepts and relationships
  Gary> (i.e. an ontology) that are somewhat generic, and thus
  Gary> applicable to multiple domains. 

This is generally correct. "Upper Ontology" is often used to describe
an ontology of highly abstract concepts (1) that is meant to be shared
among many ontologies. 

Some times, upper ontology just means the top half of an
ontology. OWL-S has been described as an upper ontology, which is why
I used terminology. 

  Gary> As such, what is referred to in Semantic MOBY as the
  Gary> "canonical graph structure" (Figure 2 in the design document
  Gary> that you referenced) is the upper ontology.

That's the thing I meant. Or, at least the vocabulary used to define
this structure. "input", "output", "mapsto" and so on. 

Oh dear. I seem to be explaining the contents of a paper which I
partly authored. This is like a comedian or cartoonist having to
explain their jokes. 

Cheers

Phil


(1) The most notorious of which are "perjurant" and "endurant"; names
    which are nearly as self-explanatory as "ortholog" and "paralog".