Pathway information is vital for understanding biological systems. Unfortunately, the over 170 online pathway data resources vary widely in coverage and representation of biological processes, making their use for biological problem solving extremely difficult. The BioPAX group was formed by the pathway database community in November 2002 to develop a standard biological pathway data exchange format to solve this issue through a series of small workshops. This has resulted in the development of the community accepted, open-source BioPAX level 1 exchange format, which supports metabolic pathway data and BioPAX level 2, which adds support for molecular interaction data. We seek support for a workshop series for the years 2006, 2007 and 2008. The goals of this meeting series are to expand the BioPAX data model by adding support for signaling pathways, gene regulation networks and genetic interactions, such as epistasis; to increase database and tool support for.BioPAX; and to encourage the growth of publicly accessible pathway data and its application to biological problems. We propose to hold BioPAX workshops twice a year, each lasting two days. These will focus on achieving our goals through BioPAX data model and community development discussions. One workshop per year will include a symposium of invited speakers discussing their pathway related computational research. Meetings will include a hackathon, where computer software, such as database converters, is collaboratively developed. Meetings will be hosted by participants and locations will cycle through SRI, Menlo Park, CA (Peter Karp), Cold Spring Harbor Labs, New York, NY (Lincoln Stein) and Memorial-Sloan Kettering Cancer Center, New York, NY (Chris Sander) or other convenient US locations. All meetings will be open to community participation and all minutes and resulting work is freely available under open source terms via the www.biopax.org website. ? ?
| Demir, Emek; Cary, Michael P; Paley, Suzanne et al. (2010) The BioPAX community standard for pathway data sharing. Nat Biotechnol 28:935-42 |
