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About Pathway Commons

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search.

  • Biologists can browse and search Pathway Commons pathways.
  • Computational biologists can download all pathways in BioPAX format for global analysis.
  • Software developers can build software on top of Pathway Commons using our web service API. You can also download and install the cPath software to create a local mirror of Pathway Commons.

All data is freely available, under the license terms of each contributing database.

About cBio @ MSKCC

The Computational Biology Center at Memorial Sloan-Kettering Cancer Center pursues computational biology research projects and the development of bioinformatics resources in the areas of:

  • sequence-structure analysis
  • gene regulation
  • molecular pathways and networks
  • diagnostic and prognostic indicators

The mission of cBio is to move the theoretical methods and genome-scale data resources of computational biology into everyday laboratory practice and use, and is reflected in the organization of cBio into research and service components -- the intention being that new computational methods created through the process of scientific inquiry should be generalized and supported as open-source and shared community resources.

About the University of Toronto

The University of Toronto is Canada's largest university, with a strong focus on research. Pathway Commons work is done in the Bader Lab.


Pathway Commons runs on cPath software, and was created by: Gary Bader, Ethan Cerami, Emek Demir, Benjamin Gross, and Chris Sander.

Pathway Commons is built entirely on open source software. We gratefully acknowledge the following open source projects.

Apache Tomcat Servlet / Java Server Pages (JSP) Engine.
Apache Commons Multiple Apache Commons projects, including DBCP: database connection pooling services.
Apache Log4j Java logging framework. Helps us track down bugs.
Apache Lucene Full-featured text search engine library. Powers all our search functionality.
Apache Struts Extensible framework for creating Java web applications. Powers all or our web pages.
ARP: Another RDF Parser RDF/XML Parser. Parses and validates all our BioPAX files.
Cruise Control Framework for running continuous builds. Re-compiles and re-tests all Pathway Commons code after every check in.
CVS Version control system.
EhCache Java caching library. Helps keep Pathway Commons running fast.
Firebug A must-have extension to Firefox, used to debug Web 2.0 applications.
JDOM Our favorite library for parsing XML in Java.
JUnit Unit test framework for regression testing.
MySQL Relational database system.
Web Developer Extension Another must-have extension to Firefox, used to debug HTML, CSS and Javascript.
Yahoo! UI Library (YUI) Web 2.0 / AJAX library. Powers all of our dynamic HTML / AJAX features. Nice work, Yahoo!


We also gratefully acknowledge Andreas Viklund, who provided the open source stylesheets, used to design the web site.