Wiki, Next conf call and presentations

[Andrea Splendiani]

Hi,
following last conf call decisions, I've restructured a little bit the
wiki:

http://neurocommons.org/page/BioPAX-OBO

there is now a space where you can describe your expertise (and
expectations ?) on the project. Please fill it (I won't start first...
I'm shy)

For next conf. call, an agenda to fill is here:

http://neurocommons.org/page/Cc-10-03-2009

ciao,
Andrea

[Oliver Ruebenacker]

Hello Andrea, All,

Thanks Andrea, I added some items to the agenda for tomorrows
BOBO-Meeting (4pm to 6pm in 346 Stata, MIT). See link and a copy of
the text below.

Take care
Oliver

http://neurocommons.org/page/Cc-10-03-2009#Agenda

== Agenda ==

=== Style ===

Suggestion (at least partially based on last time's discussion):

Set time limits to avoid open-ended discussion. Instead, have a brief
and focussed exchange of ideas, then refer to a task force to look
into the matter and report to the next meeting.

=== Topics ===

Suggestions:

- How can compounds (e.g. molecules) be identified?

- How much can a compound be changed before it turns into something
different? (e.g. different foldings, addition of small groups) Should
we allow a compound definition to be special cases of another? (e.g.
"EGFR-Dimer, phosphorylated" is special cases of "EGFR-Dimer,
regardless of phosphorylation") If we phosphorylate a protein, is it
still "the same"?

- What is the role of categorizations (e.g. "protein")? Should
categories be mutually exclusive?

- What is the role of attributes such as chemical structure or a
sequence? Should we allow patterns (e.g. XGATTACA)?

- What is the role of catalogue references (e.g. "UniProt 1234567")?

- What is the role of parts (aka components)? Does it matter whether
parts are bond covalently? Should we allow multiple competing
partitions (e.g. "A and BC" versus "AB and C")? Should we allow
patterns (e.g. "AR" with unknown "R")?

--
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