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. 2011 Jan;39(Database issue):D685-90.
doi: 10.1093/nar/gkq1039. Epub 2010 Nov 10.

Pathway Commons, a web resource for biological pathway data

Ethan G Cerami  1 , Benjamin E Gross, Emek Demir, Igor Rodchenkov, Ozgün Babur, Nadia Anwar, Nikolaus Schultz, Gary D Bader, Chris Sander
Affiliations

Pathway Commons, a web resource for biological pathway data

Ethan G Cerami et al. Nucleic Acids Res. 2011 Jan.

Abstract

Pathway Commons (http://www.pathwaycommons.org) is a collection of publicly available pathway data from multiple organisms. Pathway Commons provides a web-based interface that enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, a download site that provides integrated bulk sets of pathway information in standard or convenient formats and a web service that software developers can use to conveniently query and access all data. Database providers can share their pathway data via a common repository. Pathways include biochemical reactions, complex assembly, transport and catalysis events and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. Pathway Commons currently contains data from nine databases with over 1400 pathways and 687,000 interactions and will be continually expanded and updated.

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Figures

Figure 1.
Figure 1.
(A) Overview of Pathway Commons. Pathway Commons (http://www.pathwaycommons.org) provides a central, convenient point of access to multiple publicly available pathway and interaction databases. It does so by integrating data sources formatted in the BioPAX or PSI–MI standards, and making all data sets available via a unified web site, a single web service interface and a batch download site. (B) Pathway Commons supports multiple output formats, including BioPAX and SIF. To support SIF, we have developed a set of inference rules for converting the full BioPAX model to a simplified pairwise interaction network. Left: The full BioPAX model of the AKT pathway, shown as an SBGN process diagram (19). Upper right: the same pathway, converted to a SIF representation. Lower right: name and description of SIF rules used in the conversion. The full set of SIF rules is available on the Pathway Commons website (http://www.pathwaycommons.org/pc/sif_interaction_rules.do).
Figure 2.
Figure 2.
Neighborhood of ABCC3—a member of the superfamily of ATP-binding cassette (ABC) transporters—in Pathway Commons. Left: SIF view of the neighborhood displayed in the molecule page of Pathway Commons. Right: Process diagram of the same neighborhood drawn by ChiBE (14), which can query PC using the web service interface. It contains a single event mediated by ABCC3—transportation of glycocholate from cytoplasm to extracellular region.
See this image and copyright information in PMC

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