Scientific Advisory Board
During the November BioPAX meeting in NYC, the community agreed that the BioPAX project would benefit from a more formal process moving forward. This would include a Scientific Advisory Board and an Editorial Committee.
An initial SAB Conference Call was held on Monday, March 1st 2010 at 11.00AM (EST). Present at this meeting were; Gary Bader, University of Toronto; Peter D'Eustachio, New York University; Henning Hermjakob, European Bioinformatics Institute; Peter Karp, SRI International; Chris Sander, Memorial Sloan-Kettering Cancer Center and Carl Schaefer, National Cancer Institute; who all agreed to form and take part in a BioPAX SAB.
The current SAB board members are:
- Gary Bader, University of Toronto
- Peter D'Eustachio, New York University
- Henning Hermjakob, European Bioinformatics Institute
- Nicolas LeNovere, European Bioinformatics Institute
- Peter Karp, SRI International
- Chris Sander, Memorial Sloan-Kettering Cancer Center
- Carl Schaefer, National Cancer Institute
Editors
BioPAX Editors have a similar remit to those in other standards, mainly working with the community to motivate and expedite discussions. Major decisions on specifications are not made by editors, but rather by voting from the entire community. Editors collect all the opinions, present them to the community for discussion, and then put them on a ballot for the community to vote.
Editors are elected by the community for 3-year terms as volunteers. There is no limit on the number of terms one can serve as an editor.
In September 2010 the community voted in 3 BioPAX editors, Peter D'Eustachio, Oliver Ruebenacker and Andrea Splendiani.
In December 2011, two more editors were elected, Emek Demir and Huaiyu Mi.
Editors can be contacted through biopax-editors @ googlegroups.com e-mail address.
BioPAX People
The BioPAX project began at the Fourth BioPathways Consortium Meeting, a satellite of the ISMB'02 Conference held in Edmonton, Canada in August 2002. It was decided that a pathway exchange format would facilitate sharing of pathway information between databases and users and would be a good first step to building an open source pathway information resource. The project got underway in early October 2002 when Chris Hogue (BIND, UToronto), Peter Karp (BioCyc, SRI), and Chris Sander (MSKCC) organized the BioPAX work group. It was decided to keep the group small at first, and to expand it gradually. The initial focus of the group was the exchange of chemical compound information; and initial group members were selected with this in mind. The first BioPAX meeting was held on November 6, 2002 in New York City. During this meeting the group worked to identify the steps needed to arrive at a viable data exchange format. They also reviewed the work of other relevant groups, developed a timeline for inclusion of additional members to the BioPAX group, and began working on the problem of exchanging chemical compound information, followed by metabolic pathway representation. BioPAX Level 3 was finalized at the November 2009 meeting in NYC (NYC2009). The community is currently working on BioPAX Level 4.
Level 1
Gary D. Bader, Erik Brauner, Michael P. Cary, Robert Goldberg, Chris Hogue*, Peter Karp, Joanne Luciano, Debbie Marks, Natalia Maltsev, Eric Neumann*, Suzanne Paley, John Pick, Aviv Regev, Andrey Rzhetsky, Chris Sander, Vincent Schachter*, Imran Shah, Mustafa Syed, Jeremy Zucker
Level 2
Mirit Aladjem, Gary D. Bader, Michael P. Cary, Kam Dahlquist, Emek Demir, Peter D'Eustachio, Ken Fukuda, Frank Gibbons, Marc Gillespie, Chris Hogue*, Michael Hucka, Geeta Joshi-Tope, David Kane, Peter Karp, Christian Lemer, Joanne Luciano, Natalia Maltsev, Eric Neumann*, Suzanne Paley, Elgar Pichler, Jonathan Rees, Alan Ruttenberg, Andrey Rzhetsky, Chris Sander, Vincent Schachter*, Andrea Splendiani, Mustafa Syed, Edgar Wingender, Guanming Wu, Jeremy Zucker
Level 3
Emek Demir, Michael P Cary, Suzanne Paley, Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, Peter D'Eustachio, Carl Schaefer, Joanne Luciano, Frank Schacherer, Irma Martinez-Flores, Zhenjun Hu, Veronica Jimenez-Jacinto, Geeta Joshi-Tope, Kumaran Kandasamy, Alejandra C Lopez-Fuentes, Huaiyu Mi, Elgar Pichler, Igor Rodchenkov, Andrea Splendiani, Sasha Tkachev, Jeremy Zucker, Gopal Gopinath, Harsha Rajasimha, Ranjani Ramakrishnan, Imran Shah, Mustafa Syed, Nadia Anwar, Özgün Babur, Michael Blinov, Erik Brauner, Dan Corwin, Sylva Donaldson, Frank Gibbons, Robert Goldberg, Peter Hornbeck, Augustin Luna, Peter Murray-Rust, Eric Neumann, Oliver Ruebenacker, Matthias Samwald, Martijn van Iersel, Sarala Wimalaratne, Keith Allen, Burk Braun, Michelle Whirl-Carrillo, Kei-Hoi Cheung, Kam Dahlquist, Andrew Finney, Marc Gillespie, Elizabeth Glass, Li Gong, Robin Haw, Michael Honig, Olivier Hubaut, David Kane, Shiva Krupa, Martina Kutmon, Julie Leonard, Debbie Marks, David Merberg, Victoria Petri, Alex Pico, Dean Ravenscroft, Liya Ren, Nigam Shah, Margot Sunshine, Rebecca Tang, Ryan Whaley, Stan Letovksy, Kenneth H Buetow, Andrey Rzhetsky, Vincent Schachter, Bruno S Sobral, Ugur Dogrusoz, Shannon McWeeney, Mirit Aladjem, Ewan Birney, Julio Collado-Vides, Susumu Goto, Michael Hucka, Nicolas Le Novère, Natalia Maltsev, Akhilesh Pandey, Paul Thomas, Edgar Wingender, Peter D Karp, Chris Sander and Gary D Bader
(Nature Biotechnology 28, 935–942 (2010) paper)
BioPAX is coordinated by Chris Sander's group in the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (biopax-info@biopax.org) and Gary Bader's group at the University of Toronto, in collaboration with many of the above participants.
- - These members are only in e-mail and phone contact; others have attended BioPAX development workshops.
