==Initial Skype Transcript, formatting will follow shortly==
14/02/07 18:01
Convener: Andrea
Scribe: Andrea
Moderator: Alan
Present people: Alan, Andrea, Matthias, Dan, Harsha, Jeremy
Agenda
Nominate next Convener, scribe, moderator
Development status
Experience with text mining at Science Commons (Jonathan, Alan)
Paxtools (Emek)
Web site update [Andrea]
NCBO Grant [Alan]
Problems with ?NetPath BioPAX files
![[WWW]](/wiki/modern/img/moin-www.png)
http://www.netpath.org/ [Alan] OBI update [Alan]
Emek Congratulations
Role of the convener
Matt and Sarala examples review: Set up TC for iterested parties.
Next conference call
Next cc: 7 March
Convener: Alan
Moderator: Alan
Scribe: Andrea
Development status
Paxtools (Emek absent for personal reasons)
Experience in text mining (Alan):
goal: text-mining abstract to build network (particular relevance to ? disease). There are a few pathway database free. Goal of Science Common is to gather opensource resources, augment them with text mined info, and publishing things in like RDF/OWL (possibly biopax)
problem: text mining does not distinguish between proteins and genes.
BioPAX is not general enough to represent some text-mined information
For instance: you know whether something is a protein OR gene product... using biological entities is not appropriate.
RDF/OWL yet unefined. Using a triplestore. Need stability... (it crashes!)
In general, problems with software. (several triplestores tried)
Web site update
Alan Motion: crate IT maintenance group
responsabilities: website and mailing list, sourceforge mainetanance and development. Members should have all relevant accesses and they need to do something, and will ask for approval for major issues.
First issue: Andrea makes a test (Test = copy of wiki+web site integrated into a single one. Will show us what he comes up with).
Members: Harsha, Andrea, Alan
This is an official decision
Votes: Jeremy, Harsha, Matthias, Alan, Andrea yes: official approved.
Andrea will proceed with passords
NCBO grant:
Discussion with: Daniel, Barry, Chris. Not clear if Chris would apply independently, but this is counter-productive (Daniel's words). Better to apply with one single grant. Maybe Chris PI + co-PI. Barry interested. Need a biological focus.
What will biopax be useful for ?
Jeremy: integration of pathway databases Harsha: inter-operation of databases too
14/02/07 18:34
National Cancer Institute (NCI), (
http://www.nci.nih.gov) National Heart, Lung, and Blood Institute (NHLBI), (
http://www.nhlbi.nih.gov/) National Institute on Alcohol Abuse and Alcoholism (NIAAA), (
http://www.niaaa.nih.gov/) National Institute of Biomedical Imaging and Bioengineering (NIBIB), (
http://www.nibib.nih.gov/) National Institute of Dental and Craniofacial Research (NIDCR), (
http://www.nidcr.nih.gov/) National Institute of Environmental Health Sciences (NIEHS), (
http://www.niehs.nih.gov/) National Institute of General Medical Sciences (NIGMS), (
http://www.nigms.nih.gov/) National Institute of Mental Health (NIMH), (
http://www.nimh.nih.gov/) National Institute of Neurological Disorders and Stroke (NINDS), (
http://www.ninds.nih.gov/) National Institute on Drug Abuse (NIDA), (
http://www.nida.nih.gov/)
Scientific case should be of interest of one of the above
Jeremy point: usefulness of the integraton of HumanCyc, Reactome and Pallson metabolome.
Can't just be a computational model, need to address some biological question
Questions that cannot be answered WITHOUT biopax OR questions that are hard to answer without biopax?
PI should be from US (bio - PI)
Task: find a real biological use case intersting to one or more of the above groups. Brainstormig + ask the program leaders for use cases.
next week: meeting for grant discussion ? JeremyZucker 14/02/07 18:43 Brainstorming ideas:
Adult stem cells when given a metabolite, divide rapidly. when the vitamin is removed, it returns to normal. Why?
http://web.mit.edu/newsoffice/2003/sherley.html
next grant meeting: include Harsha
Problems with NetPath
biopax files: bugged
(need to be fixed) send feedback ?
OBI update
Alan will send a note about it.
http://obi.sourceforge.net/index.php
idea: something of OBI should be used in biopax. They also deal with hypothesis, conclusions, methods... (could be used in biopax annotations)
https://www.cbil.upenn.edu/obiwiki/index.php/Milestones
Role of convener:
setup the meeting AND THE AGENDA (note for Andrea)
Matt and Sarala examples review:
they are in New Zeland, so standard conference time is not good.
From: ![[MAILTO]](/wiki/modern/img/moin-email.png){kind=small}
matt.halstead@auckland.ac.nz Subject: [BioPAX-discuss] Biopax level 3 Date: February 8, 2007 2:06:29 AM EST To: biopax-discuss@cbio.mskcc.org
Hi all,
Sarala Dissanayake and I are looking at various notes in the Biopax Wiki about proposals for the next biopax - whether that is a level 3 or something else I am not sure. At the moment we are centered around the States and Generics proposal ( http://biopaxwiki.org/cgi-bin/moin.cgi/StatesAndGenericsProposal) because for our area of modelling (mainly cell signalling and electrophysiology) we were inventing our own additions to Biopax level 2, but saw the same intentions coming up in the StatesAndGenerics proposal.
We are now using the owl file on that wiki page as our basis for building our models.
However, I do not understand the relationship of this model to other discussions on the mailing list, for example:
http://cbio.mskcc.org/mailman/private/biopax-discuss/2007-January/001974.html
or to the wiki, for example:
http://biopaxwiki.org/cgi-bin/moin.cgi/Alanr_Level_2_or_3_Proposal
We realise this is a volatile area of the biopax specifications, but are wondering what was the best starting point for us and the best single point resource which would provide the most up to date and linear description of the new specification in consideration.
I also assume that we will start have quite a few questions about the proposals. Sarala already has examples she has done using the StatesAndGenerics proposals which would be useful to have feedback on, but we are not sure if this StatesAndGenerics proposal still has a following that would be interested in looking through these.
kind regards Matt