Pathway Commons 2

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Gary Bader

Nov 19, 2013, 4:26:28 PM11/19/13
A completely new version of Pathway Commons is now available at

Pathway Commons is a collection of publicly available pathways, currently containing 6 pathway and interaction databases, focused on human. These are: Reactome, NCI Pathway Interaction Database, PhosphoSitePlus, HumanCyc, HPRD and PANTHER. We will add more databases in the future.

What’s new? Lots!
• Completely rewritten software system three years in the making.
• Supports metabolism, gene regulation, molecular and genetic interactions, and signaling, including molecular states (e.g. phosphorylation TP53), generic molecules (e.g. Wnt family of proteins) with BioPAX Level 3
• Visualize pathways and networks in your web browser using the new PCViz system. At
• Download pathways and networks from Pathway Commons in Cytoscape for analysis using the new CyPath2 app for Cytoscape 3
• Pathway viewer and editor linked to Pathway Commons, called ChiBE, at
• For computational biologists and software developers
• PC2 Web service: advanced graph queries; normalized and up-to-date data; resolvable URIs (<version>/*); programmatic access; batch downloads (; Linked Data ready: and See data versions currently loaded at
• Standard language for Biological Pathway Exchange and a software library for handling data (BioPAX & Paxtools).
• Previous Pathway Commons website is still available at However, it is now static.

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The Pathway Commons Team

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