Agenda: Bridging BFO, SBO and SBPAX?

[Oliver Ruebenacker]

Hello, All,

My suggestion for agenda today: Bridging SBO, BFO and SBPAX
(identifying relationships such as: identity, subclass, subproperty,
or distinctness)

Ideas?

Take care
Oliver

--
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

[Andrea Splendiani]

I'll wait for your introduction ;)

On a related subject, I'm dealing the a simple, yet tricking, modeling
case, I'll write more in another email.

ciao,
Andrea

Il giorno 10/feb/09, alle ore 19:48, Oliver Ruebenacker ha scritto:

-----------
Andrea Splendiani
post-doc, bootstrep project (www.bootstrep.eu)

UPRES-EA 3888 - Laboratoire d'Informatique Médicale
CHU de Pontchaillou
2, rue Henri Le Guilloux
35033 Rennes - France
Tel : +33 2 99 28 92 45 / +33 2 99 28 42 15 (secr.)
Fax : +33 2 99 28 41 60

48° 07.275N
1° 41.643W

[Andrea Splendiani]

Hi,

I'm dealing with a simple modeling case, yet tricky.

I have a set of basic facts that report that a gene is involved in an
host-parasite process, by reporting phenotypic variation as
consequences of its "knock out".
Using only a phenotype ontology won't be enough, as phenotypes can be
things as resistance to drug, the drug being an information known...

I was thinking about describing a canonical organism where the
pathogen induces the disease, and a variation (ko) where the disease
quality is changed. However, what I have is actually a relative
variation.

If somebody has seen something similar and has some hints, hints are
welcome.

ciao,
Andrea

[Oliver Ruebenacker]

Hello, Andrea, All,

You mean basically how to get from "The grass is green" to "The
grass is green when the sun shines"? Sounds like an interesting
fundamental problem.

We can put it on the agenda and split time, how about that?

Take care
Oliver

[Michel Dumontier]

Andrea,

  We've dealt with this in our yeast ontology that integrates SGD data. See the paper:

http://dx.doi.org/10.1016/j.jbi.2008.05.001

-=Michel=-

On Tue, Feb 10, 2009 at 2:05 PM, Andrea Splendiani <andrea.s...@univ-rennes1.fr> wrote:

--
Michel Dumontier
Assistant Professor of Bioinformatics
http://dumontierlab.com

[Andrea Splendiani]

Ok, cannot access it from home, I'll see if I'll have more chance tomorrow at the office.

ciao,

Andrea

Il giorno 10/feb/09, alle ore 20:44, Michel Dumontier ha scritto:

[Oliver Ruebenacker]

Hello,

Alan is on the way here with his laptop. My laptop has some
connection problems. So, hopefully, we will start meeting soon.

Take care
Oliver

[Andrea Splendiani]

I'm online for another hour or so...

ciao,
Andrea

Il giorno 10/feb/09, alle ore 22:05, Oliver Ruebenacker ha scritto: