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What's New:

  • New!  May 28, 2013:
    • This portal will not be updated in the future and we are working on a replacement Pathway Commons service for expected release in mid-2013.
    • We encourage you to test the new service and switch to it once it is released.
    • Please send us questions and feedback.
  • Oct 27, 2011:
    • BioGRID data set (September 25, 2011 Version 3.1.81).
    • IntAct data set (September 29, 2011 Version 3.1.17288).
    • Nature Pathway Interaction data set (October 12, 2011).
    • Reactome data set (September 20, 2011 Version 38).
  • June 24, 2011:
    • BioGRID data set (May 1, 2011 Version 3.1.76).
    • HumanCyc data set (June 8, 2011 Version 15.1).
    • Nature Pathway Interaction data set (June 14, 2011).
  • April 25, 2011:
    • Reactome data set (March 15, 2011 Version 36).
    • IntAct data set (February 3, 2011 Version 138).
    • MetaCyc removed due to organism generic pathways - will be brought back when these pathways are supported in Pathway Commons.
    • Bug fixes to import pipeline and batch download exporter.
  • February 4, 2010:
    • Added MetaCyc data set (December 7, 2010 Version 14.6).
    • BioGRID data set (December 15, 2010 Version 3.1.72).
    • HumanCyc data set (October 7, 2010 Version 14.6).
    • IntAct data set (December 15, 2010).
    • Mint data set (December 21, 2010).
    • Nature PID (September 16, 2010).
    • Reactome data set (December 17, 2010 Version 35).
  • September 7, 2010:
    • BioGRID data set (July 31, 2010 Velsion 30.0.67).
    • HPRD data set (April 13, 2010 Version 9).
    • HumanCyc data set (June 16, 2010 Version 14.1).
    • IntAct data set (August 8, 2010).
    • MINT data set (July 28, 2010).
    • NCI/Nature Pathway Interaction Database (August 10, 2010).
    • Reactome data set (June 18, 2010 Version 33).
  • October 15, 2009:
    • Improved search functionality.
  • July 2, 2009:
    • Batch Download of all Pathway Commons data in multiple file formats is now available.
    • Systems Biology Center New York - IMID data set (December 17, 2008 Version 27).
    • Latest Reactome data set (June 24, 2009 Version 29).
    • Latest HumanCyc data set (June 22, 2009 Version 13.1).
    • All yeast proteins are now annotated with UniProt functional annotation.
 

Using Pathway Commons:

Biologists: Browse and search pathways across multiple valuable public pathway databases.

Computational biologists: Download an integrated set of pathways in BioPAX format for global analysis.

Software developers: Build software on top of Pathway Commons using our web service API. Download and install the cPath software to create a local mirror.

Current Data Sources:

Pathway Commons currently contains the following data sources (batch download):

Pathway Commons Quick Stats:
Number of Pathways: 1,668
Number of Interactions: 442,182
Number of Physical Entities: 86,282
Number of Organisms: 414

Integration of additional data sources is planned in the near future. For a comprehensive directory of interaction and pathway databases, please refer to Pathguide.

Citing Pathway Commons:

To cite the Pathway Commons Project: Cerami et al. Pathway Commons, a web resource for biological pathway data. Nucl. Acids Res. (2010) doi: 10.1093/nar/gkq1039

To cite the cPath Software: Cerami et al. cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics. (2006) doi:10.1186/1471-2105-7-497