PathwayCommons web service API

PathwayCommons web service API provides programmatic access to an integrated collection of pathway and molecular interaction data to enable retrieval and computational analysis of biological networks.

Key Features:

• Integrated data model: Integrates publicly available pathway and molecular interaction data from multiple organisms into a unified model.
• Standard formats: Supports BioPAX and PSI-MI to ensure interoperability across pathway databases.
• Data coverage: Aggregates data from nine databases comprising over 1,400 pathways and more than 687,000 interactions.
• Event and entity types: Represents biochemical reactions, complex assembly, transport, catalysis, and physical interactions involving proteins, DNA, RNA, small molecules, and complexes.
• Programmatic access: Exposes a web service API for querying and retrieving integrated pathway and interaction data.
• Bulk downloads: Provides integrated bulk downloads of pathway information in BioPAX and PSI-MI formats.

Scientific Applications:

• Systems biology: Enables analysis and modeling of complex biological networks.
• Drug discovery: Supports network-based investigation of targets, pathways, and molecular interactions relevant to drug research.
• Molecular interaction studies: Facilitates large-scale interrogation of protein–protein, protein–DNA, protein–RNA, and small-molecule interactions.

Methodology:

Integrates publicly available pathway and molecular interaction data into a unified model, standardizes data to BioPAX and PSI-MI, and exposes the integrated dataset via a web service API and bulk downloads.