Correction: Meeting Friday 3 Feburary 2006
jonath...@gmail.com
BioPAX Boston meeting
Friday, 3 February 2006, 3:00 pm to 5:00 pm
MIT, Stata Center, room 346
Agenda: Work on the E. coli metabolic network comparison, if either
Jeremy or Alan shows up. Otherwise, probably a study group on how to
use BioPAX and BioPAX content from programs.
Directions to Stata:
https://www.csail.mit.edu/contact/contact.html
Map showing Stata:
http://whereis.mit.edu/map-jpg?selection=32&Buildings=go
Map showing room 346:
https://www.csail.mit.edu/resources/maps/3/346.gif
One way to get to 346 (once you're at Stata):
1. Go to the EAST (Main St) bank of elevators.
2. Take an elevator to the third floor.
3. As you leave the elevator, turn to your right and go through the
double doors.
4. Go left, then left again immeddiately, then straight. 346 is
directly ahead.
Alan Ruttenberg
Questions we are wrestling with:
1) Ecocyc labels a bunch of things as small molecules that are not (I
posted about this on the discuss list). How *should* these be modeled?
2) Neither none of KEGG ids, CAS numbers nor SMILES are unique
identifiers small molecules found there, in particular isomers often
share ids, charged states are another issue, and there are also
errors that result in this. Can we model this? Do we have to throw
away the power of merging DBs based on these identifiers? Should they
be fixed before being exported to BioPAX?
3) How would we approach modeling small molecules as classes instead
of instances, as we have done so far? What are the implications for
merging?
-Alan
Dan Corwin
3) How would we approach modeling small molecules as classes instead of instances, as we have done so far? What are the implications for merging?
Q1) For Subject, S, which true predicate(s) would make S a "class"?
Q2) What would the other possible combo(s) model, in your lexicon?
Dan
If cannot read this, try http://www.lexikos.com/exhibit/cms/shared/radio.html
jonath...@gmail.com
comprehensive. See you in June! - Jonathan
- Joanne is convenor of the next meeting. Date, time, location, agenda
are up to her.
Pavel from IT-omics was introduced and gave a demo of LSGRAPH.
Looked at E coli network unification again:
What advice should BioPAX give to database providers?
What advice should BioPAX give to people trying to combine databases?
E.g. if we find
entity CAS KEGG
A 123 C5
B 123 C7
what do we do? Flag as error, put in patch file?
Or relax assumptions?
maybe two different smallMolecules can have the same CAS?
maybe two different smallMolecules can have the same KEGG?
Discussed nature of CAS id's.
SMILES is not unique to enantioisomer. Need isomeric SMILES.
Joanne Luciano
With the urgent need to get BioPAX governance
resolved so that we can make decisions and receive
funds it may serve us well to attend the discussion
tonight at the Harvard COOP.
The discussion starts at 7, and we can meet before at the Coop Bookstore
Café at 6:00. Then we can discuss meeting times and topics
for the next meeting and who'd like to be the next convenor.
I'm happy to do it this month, but approx March 1 I head
to the other side of the Pond until mid April when
I will be back for 2 weeks.
Those interested in further discussions
afterward the discussion at the COOP can decide on venue
and head over for dinner or brew. John Harvard's Brew Pub
is always good for what ales ya <wink>.
--------------------------------------------------------
This week's BioPAX-Boston Meeting will
be centered around the Harvard COOP Author Event:
http://www.harvardsquare.com/eventdesc.php?id=71079
Governing Nonprofit Organizations
Federal and State Law and Regulation
Discussion
Author: Marion Fremont-Smith
Harvard COOP
1400 Massachusetts Avenue - 3rd floor
Cambridge, MA 02138
617 499-2000
http://maps.google.com/maps?output=setprefs&near=1400%20Massachusetts%20Ave,
%20Cambridge,%20MA%2002138
Hope you can make it.
Joanne
-----------------------------------------------------
Dan Corwin
Best,
Dan
zucker
Will be unable to make today's meeting. I really don't understand the
details of the funding issues that were brought up at the conference
call. It seems to me that the argument was that a PI is required for
academic grants, and that the PI is ultimately responsible for the
distribution of funds. The relationship and responsibilities of the PI
to the BioPAX community therefore has to be made explicit, particularly
as regards the decision-making authority that is delegated to the PI.
Sincerely,
Jeremy
Joanne Luciano
Authority (because it was delegated to the community). This not a good
position to be in and has to be handled carefully ahead of time. If the PI
disagrees with the community because of his/her own interests or commitments
then there's a conflict of interest.
That is why I proposed that BioPAX be an independent organization with its
own governance. This way anyone who wants to work on BioPAX can and if a PI
wants to put in a grant for BioPAX they put in a grant for participating or
developing what they want. So for example, the caBIG / Cytoscape work is to
enhance Cytoscape and deliver a DB in the format to NCI, the PATIKA grant is
to build tools that utilize BioPAX etc. But none of those PIs own or make
decisions on their own for BioPAX. Also if one wants to put in the budget
to host a BioPAX workshop that's fine too.
So to me that separates the authority and responsibility nicely.
An independent organization is then free to obtain funding and sponsorship
for itself without concern for bias, which has to be explicit with the
sponsors/funders also.
I'm ccing the BioPAX-Admin (dev) list because we agreed on the conference
call to discuss this there. I'd also like to propose that we set up time to
discuss these issues. We are overdue for a BioPAX-admin conference call. I
don't know about you, but I'm overwhelmed with email lists and already am
behind a few weeks.
How about next Wednesday Feb 15th at noon. This is a time that seems to work
for the BioPAX monthly calls, perhaps it will work here.
Below I've pasted the portion of the minutes that discusses governance
(Minutes:
http://biopaxwiki.org/cgi-bin/moin.cgi/2006-02-08_Conference_Call_Minutes)
Motion to endorse BioPAX Governance. Discussion [WWW] here (Jonathan/Alan)
Emek - the document doesn't match well with the current funding mechanism,
which is academic-focused (NIH), which means there is a PI. PI responsible
for funds inconsistent with group make decisions.
Ken - can't see a way to include funding issues - the governance document is
based on trust. He doesn't think there can be a clear modification that can
solve the funding issues, because funding has their own restrictions.
Jonathan - we just need transparency.
Alan - Distinction between requesting funding on behalf of BioPAX versus
funding to participate in BioPAX. Former is a group process (possibly
delegated) latter anyone can do.
Joanne thinks that anyone can propose a workshop. Her proposal is that
BioPAX can form a consortium and apply for funding. Funding so far has been
academic - won't stay that way.
Joanne - Trust hasn't worked well for her - issue of consulting fees due her
from previous grant.
Jonathan: "how about biopax can't take funding at all? Or make a
corporation, or steering committee? risk: people will take advantage of
biopax to do their own stuff.e.g. Jonathan gets a grant to develop biopax;
then takes the money and runs on some random track that differs from what
the group wants.
Alan worries that unless there is coordination, multiple groups might apply
for funding for similar "BioPAX" confusing/turning off funders.
Ken suggests that Sander group comes up with a proposal. He will also
contribute from his own experience.
Take it offline on the dev list. Ken, Emek, Gary, Joanne, Jonathan, Alan,
Jeremy. Some proposed wording in the next two weeks.
Joanne
P.S. I cc'd Emek as I'm not sure he's on the biopax-boston or dev lists but
is in the minutes as having interest.
Alan Ruttenberg
This sounds very interesting and apropos. Unfortunately it's
difficult for me to take an evening slot without more advance
planning. I'd appreciate it if someone who attends could take notes
and post them to the list.
-Alan
Joanne Luciano
My apologies for the short notice.
I didn't learn I was convenor until Tuesday and I didn't have time to think
about the meeting or sort out how to reserve a room. It wasn't until last
night that I learned about the talk at the COOP, but got excited because
it's
on topic. If the book looks good and the discussion is good I'll pick up a
copy.
Joanne
> -----Original Message-----
> From: BioPAX...@googlegroups.com
> [mailto:BioPAX...@googlegroups.com] On Behalf Of Alan Ruttenberg
> Sent: Thursday, February 09, 2006 11:42 AM
> To: BioPAX...@googlegroups.com
> Subject: Re: Thursday Feb 9th 6:00 PM Harvard COOP / Meet up 7PM Talk
>
>
Frank Schacherer
Frank
Joanne Luciano
Sorry about the short notice. I wish I knew about it ahead of time.
If anyone is coming let me know else I'll skip the 6pm and just head over
for 7.
I'll report back on the discussion and we can set up the next meeting.
Have a good evening.
Joanne
> -----Original Message-----
> From: BioPAX...@googlegroups.com
> [mailto:BioPAX...@googlegroups.com] On Behalf Of Frank Schacherer
> Sent: Thursday, February 09, 2006 2:31 PM
> To: BioPAX...@googlegroups.com
> Subject: Re: Thursday Feb 9th 6:00 PM Harvard COOP / Meetup 7PM Talk
>
>