The Integrated Interactions Database lets users search interaction data by gene or protein identifiers and organism.
Pathway Commons
Pathway Commons provides access to data integrated from public pathway and molecular interaction databases.
About Pathway Commons
Pathway Commons is a web resource for biological pathway analysis. It collects and integrates data from public pathway and molecular interaction databases and represents it in the Biological Pathway Exchange (BioPAX) standard. The data covers biochemical reactions, gene regulatory networks, genetic interactions, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes.
On the site you can search and view pathways and interactions, with sample visualizations in search results. Data can be downloaded in BioPAX, Simple Interaction Format (SIF), and Gene Set Database (GMT) formats, available per data source. Programmatic access is provided through BioPAX and SIF web services and a SPARQL endpoint. Related tools include PCViz for visualization, CyPath2 for Cytoscape, PaxToolsR for R, and ChiBE for viewing and editing BioPAX models. A Guide section provides workflows and primers for pathway analysis.
The site suits researchers working with gene expression data and software developers building pathway analysis tools.
Key features
- Search and view integrated pathways and molecular interactions
- Download data in BioPAX, SIF and GMT formats
- Access data via BioPAX and SIF web services
- Query data through SPARQL endpoint
- Use with Cytoscape, R and ChiBE tools
- Guide with workflows and primers for pathway analysis
Best for: Researchers and software developers working with biological pathway and interaction data.
Good for
- Data integrated from multiple public pathway databases
- Data is free and provided software is open-source
- Multiple download formats and programmatic access options
- Includes guide with workflows and primers
Watch out for
- Includes only databases freely available for academics
- Downloads and formats vary by data source
Pathway Commons at a glance
- Website
- pathwaycommons.org
- Category
- Research & Data › Open Data & Datasets
- Type
- Website
- Pricing
- Free
- Platforms
- Web
- Open source
- Not stated
- Language
- English
- Last checked
- Oct 5, 2026 · Online when checked
- Listed
- Oct 5, 2026
Pathway Commons alternatives
Tools and sites you could use instead, ranked by how closely they match.
Reciprocal Net links a distributed crystallography network with a searchable collection of common molecular structures.
The Rat Genome Database provides integrated genetic, genomic, physiological, pathway, and disease information with research tools.
PHI-base curates molecular and biological information on genes affecting pathogen-host interactions and some anti-infective targets.
PathCards integrates human biological pathway databases and annotations into unified pathway records.
Browse Kurucz atomic line lists alongside links to related astronomy and molecular databases.
Popular in Open Data & Datasets
Well-known listings from the same topic.
data.worlddata.worldNASA APIapi.nasa.govCosmoSimcosmosim.orgdata.meudon.frdata.meudon.frESS-DIVEess-dive.lbl.govState of Hawaiidata.hawaii.gov
Pathway Commons FAQ
What is Pathway Commons?
It collects and disseminates biological pathway and interaction data from partner databases, represented in the BioPAX standard.
Is Pathway Commons free to use?
Yes. All data provided by Pathway Commons is free, and all software it provides is open-source.
How can I access Pathway Commons data?
You can search and view on the web, use ChiBE, Cytoscape or R, or use web services and the SPARQL endpoint.
Is something wrong or out of date?
Tell us and an editor will check it.
Own this website?
Claim this listing
Claim the listing and suggest updates yourself. An editor checks every claim first.