Pathway Commons (PC) integrates a number of biological pathway and molecular interaction databases into one large BioPAX model. The PC Web API described below can be used by computational biologists to download subsets of Pathway Commons for analysis, or to incorporate powerful biological pathway and network information retrieval and query functionality into websites and other software.

This tutorial has some limitations:

• It provides less information than can be found on the PC web service home page.
• Queries timeout after 10 seconds; opening a request URL in a new tab overcomes this limitation.
• It does not cover all available API functions or parameters.
• Only one parameter value is supported for functions that can accept an array for given parameter.

Useful PC and BioPAX tools that we support:

• The Java client library.
• The Paxtools library (official BioPAX Java API and data model).
• The Javascript client library.
• The Paxtoolsr R package provides added functionality for interacting with data retrieved via the PC web service.