What BioPAX communicates and how to extend OWL to help it (was: BioPAX Boston meeting, 11 October 2007)
Oliver Ruebenacker
I think the paper accurately describes the tensions surrounding
BioPAX and I like the proposals to extend OWL with one caveat: I would
not propose them as extensions of OWL, but as a separate layer.
The extensions are very useful and easily implemented in principle,
but deeply clash with OWL principles. As the authors understand, they
do not freely blend with OWL reasoning. The suggested restrictions do
not behave like established OWL restrictions:
- Usually in OWL, class restrictions are inherited to subclasses,
but the suggested restriction of no direct instances is not.
- Usually, OWL reasoning can continue at any point, but some
proposed extensions are intended to be used after established OWL
reasoning has finished.
- Usually, OWL reasoning does not identify something as incomplete,
because in an open world there always might be data somewhere that
completes it
Therefore, I suggest to introduce the extensions as a separate
layer: They deserve their own name (maybe OWLCAGE?) and their own
syntax to avoid confusion.
OWLCAGE reasoning builds on OWL reasoning and introduces new
assumptions. While OWL makes only conclusions that are still valid
when new data is added (open world assumption), OWLCAGE reasoning
makes conclusions valid only for a certain set of data (closed world
assumption). While OWL has no notion of completeness, OWLCAGE has a
well-defined notion that the present set of data is complete for a
particular purpose.
Take care
Oliver
On 10/10/07, Dan Corwin <d...@lexikos.com> wrote:
>
> Hi All -
>
> The "attitudes" in this paper seem most relevant to our planned
> discussion, and I believe they point us toward 3 excellent avenues
> for BioPAX's evolution and growth.
>
> http://www.webont.org/owled/2006/acceptedLong/submission_26.pdf
>
> I hope all those meeting tomorrow will have read about them.
>
> Dan
>
>
> jonath...@gmail.com wrote:
> > The meeting will be:
> >
> > Thursday, 11 October 2007, from 3:00pm to 5:00pm EDT.
> > Location: Stata G451, MIT.
> >
> > The Stata Center is the huge Gehry building at the corner of Vassar
> > and Main in Cambridge.
> > G451 is on the 4th floor very close to the east (= Gates = Main St)
> > elevator bank. From the elevators go short distances straight, left,
> > right, right, straight; see floor plan at
> > http://www.csail.mit.edu/resources/maps/4G/G451.gif .
> >
> > We'll discuss the relations between BioPAX, the semantic web, and OBO
> > (especially OBI and OBO Foundry).
> >
> >
> > >
> >
>
> >
>
--
Oliver Ruebenacker, Post-Doc Researcher
Theoretical Biological Physics and Soft Statistical Mechanics
Cell Biology at UConn Health Center and Physics at Harvard
http://people.deas.harvard.edu/~oliver/