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Pathway Commons

Pathway Commons (PC) is a convenient single point of access for all publicly accessible pathway information and BioPAX the cornerstone of standardization efforts. The long-term vision is to achieve a complete computable map of the cell across all species and conditions. We aim to provide for the efficient exchange of pathway data; aggregation and integration into a shared public information store; distribution in a value-added, standardized form; and availability to the end-user in the context of domain-specific portals, such as genomics, model organism and bioinformatics web portals, via advanced internet web service technology.

Goals

1. Maintain and extend the BioPAX ontology.
2. Further develop and maintain free software for reading, writing, aggregating, exposing, querying and analyzing pathway data.
3. Provide next-generation user-centric internet access to the PC resource and continuously aggregate, validate and integrate pathways from major available sources.
4. Disseminate the technology of biological knowledge representation and pathway analysis by collaboration and training.

This effort builds on the recent emergence of a diverse and active community of pathway databases, the development in this community of a common language for biological pathway data exchange (BioPAX) and over 30 FTE-years of work in the Sander and Bader groups since late 2002 in building infrastructure for managing, integrating, and analyzing pathway information.

PC does not compete with or duplicate the efforts of pathway database providers, but adds value to these efforts.

Funding and publications

Pathway Commons: Research Resource for Biological Pathways, PIs: Chris Sander, Gary Bader, 1U41HG006623 (formerly 1 P41 P41HG04118)

Pathway Commons, a web resource for biological pathway data, Ethan G. Cerami; Benjamin E. Gross; Emek Demir; Igor Rodchenkov; Ozgun Babur; Nadia Anwar; Nikolaus Schultz; Gary D. Bader; Chris Sander, Nucleic Acids Research 2011; doi: 10.1093/nar/gkq1039

BioPAX - A Community Standard for Pathway Data Sharing, Michael Cary et al. (multiple authors), Nature Biotechnology 28, 9 (2010).

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Related Projects

Pathway Commons team also develop or actively contribute to the following projects:

• Pathway Commons and BioPAX core plugins for Cytoscape v2 and v3;
• Pathway Commons 2 app for Cytoscape 3: CyPath2;
• BioPAX, hosted at http://sourceforge.net/projects/biopax/, including -
  • Paxtools
  • The BioPAX Validator
• The cBio Cancer Genomics Portal, http://code.google.com/p/cbio-cancer-genomics-portal/
• ChIBE, http://code.google.com/p/chibe/
• BP Prior
• Factoid
• SBGN
• COMBINE
• Help, discuss, import/share BioPAX and ontology data with Reactome, PANTHER, NCI_Nature (PID), PhosphoSitePlus, MIRIAM (EBI), Identifiers.org, Bio2Rdf, and others.

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Issue Updates

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