Pathway Commons is a web resource that provides publicly available biological pathway data from multiple organisms. It offers a web-based interface for browsing and searching pathways, a download site for integrated pathway information, and a web service for querying and accessing data. The database integrates data from nine public databases, containing over 1400 pathways and 687,000 interactions. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It uses the BioPAX format for data collection and provides data in various formats, including BioPAX, SIF, and OWL (RDF/XML). The system allows users to search for pathways and molecules, and provides tools for network analysis and visualization. Pathway Commons also offers a web service for programmatic access to pathway data. The database is supported by a community of pathway data providers, and aims to improve data integration through standardized practices and tools. Pathway Commons is implemented using open-source software and is continuously updated to include new data and improve functionality. The database is freely available and provides tools for researchers to access and analyze biological pathway data.Pathway Commons is a web resource that provides publicly available biological pathway data from multiple organisms. It offers a web-based interface for browsing and searching pathways, a download site for integrated pathway information, and a web service for querying and accessing data. The database integrates data from nine public databases, containing over 1400 pathways and 687,000 interactions. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It uses the BioPAX format for data collection and provides data in various formats, including BioPAX, SIF, and OWL (RDF/XML). The system allows users to search for pathways and molecules, and provides tools for network analysis and visualization. Pathway Commons also offers a web service for programmatic access to pathway data. The database is supported by a community of pathway data providers, and aims to improve data integration through standardized practices and tools. Pathway Commons is implemented using open-source software and is continuously updated to include new data and improve functionality. The database is freely available and provides tools for researchers to access and analyze biological pathway data.