A completely new version of Pathway Commons is now available at http://www.pathwaycommons.org

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 http://www.pathwaycommons.org/pcviz/
• 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 https://code.google.com/p/chibe/

Also for computational biologists and software developers:

• PC2 Web service:
• advanced graph queries
• Normalized and up-to-date data
• Resolvable URIs (http://purl.org/pc2/<version>/*)
• Programmatic access
• Batch downloads at http://www.pathwaycommons.org/pc2/downloads.html
• Linked Data: http://purl.org/pc2/sparql and http://purl.org/pc2/fct
• Standard language for Biological Pathway Exchange and a software library for handling data (BioPAX & Paxtools). http://www.biopax.org/
• Previous Pathway Commons website is still available at http://www.pathwaycommons.org/pc/ However, it is now static.

Send us your feedback at http://www.pathwaycommons.org/pc/get_feedback.do

Follow us on Twitter for updates: http://twitter.com/PathwayCommons

Thanks!

The Pathway Commons Team