Version 8: Over 42 000 Pathways and 1 350 000 Interactions from 22 Data Sources

Pathway Commons

Pathway information. Single point of access.

Pathway Commons aims to store and disseminate knowledge about biological pathways. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely available under the license terms of each contributing database.

Pathway Commons, a web resource for biological pathway data. Cerami E et al. Nucleic Acids Research (2011).



Visualize, Edit, and Analyze Pathways.

PCViz Logo

Pathway Viewer Web

Search by gene name
View pathway neighbors


BioPAX Editor Desktop

View BioPAX-encoded pathways
Visually edit BioPAX

CyPath2 Logo

PC Analyzer Cytoscape

Access Pathway Commons
Search and query webservice


Computational Biologists & Software Developers

Build apps. Dig into BioPAX. Use R.

Pathway Commons 2 Logo


BioPAX level 3 integrated data
Programmatic access

PC Web Service
Paxtools Logo

BioPAX Java

Language specification
PaxTools Java library

R Logo

PC Analyzer R

Bioconductor package
BioPAX editing

RDF logo


PC BioPAX integrated data -
SPARQL endpoint and Faceted browser

PC for LinkedData
BioPAX Logo

BioPAX ValidatorWeb, Java

Validate your BioPAX models
Web and console tool for pathway data authors

BioPAX Validator

Frequently Asked Questions

What is Pathway Commons?

Pathway Commons is a collection of publicly available pathway information from multiple organisms. It provides researchers with convenient access to a comprehensive collection of biological pathways from multiple sources represented in a common language for gene and metabolic pathway analysis. Access is via a web portal for query and download. Database providers can share their pathway data via a common repository and avoid duplication of effort and reduce software development costs. Bioinformatics software developers can increase efficiency by sharing pathway analysis software components. Pathways can include biochemical reactions, complex assembly, transport and catalysis events, physical interactions involving proteins, DNA, RNA, small molecules and complexes, gene regulation events and genetic interactions involving genes.

Yes, the Pathway Commons data are available for free! Pathway Commons distributes pathway information with the intellectual property restrictions of the source database. However, only databases that are freely available or free to academics are included. Additionally, this site provides several free pathway analysis software examples to conduct gene pathway analysis.

No. Pathway Commons does not compete with or duplicate efforts of pathway databases or software tool providers. Pathway Commons will add value to these existing efforts by providing a shared resource for publishing, distributing, querying, and analyzing pathway information. Existing database groups will provide pathway curation, Pathway Commons will provide a mechanism and the technology for sharing. A key aspect of Pathway Commons is clear author attribution. Curation teams at existing databases must be supported by researchers to ensure they can keep performing their valuable work.

The Pathway Commons work group will continue to provide software systems to collect, store and integrate pathway data from database groups, with clear author attribution; store, validate, index and maintain the information to enable efficient, quality access; distribute pathway information to the scientific public; and, provide a basic set of end user software for querying and analysis of metabolic and gene pathways. We will be adding more databases over time.

BioPAX, or Biological Pathway Exchange, is a standard exchange format for biological pathways. Pathway databases that make their data available in this format can be imported into Pathway Commons. BioPAX is developed through a collaborative effort by many pathway databases. More information is available at http://biopax.org.

Benefits of exporting your data to BioPAX and distributing it via Pathway Commons include:

  • Your data will be used more: Through BioPAX and Pathway Commons, your data can reach more places, including many projects that rely on BioPAX for pathway data import and analysis. We pay attention to ensuring that you are clearly identified as the original data source so that you can receive credit. We log our website usage per data source and provide it back to you for your reporting needs.
  • You will get more feedback and help with quality control: You can use the BioPAX validator to check your data against more than a hundred rules. We also automatically and manually check your exported data every release. Users of Pathway Commons often offer great feedback and whenever relevant we pass them back to you.
  • Your data will be compatible with a range of software tools: There are more than 40 active tools that support BioPAX. Do you need web based visualization? You can use PCViz. Do you need graph and pattern searches? There are existing libraries for that. Do you want to use your data in Cytoscape or R? There are multiple apps that support BioPAX.
  • We help you build your website and software tools: You will be able to automatically export your data to many other standard formats through BioPAX to e.g. SBGN, SBML, GSEA, SIF and linked data (RDF). Multiple software components are available to support more rapid application development, such as the powerful PaxTools Java library.
  • Engage with a community of Pathway Informatics researchers: A key component of the BioPAX community is Pathway Data Providers like you. Through our online forums and face to face meetings, we were able to catalyze excellent convergence and interoperability between pathway databases and software tools. Comparing your data schema against others can give you excellent insights and an opportunity to introduce your ideas to other researchers.
  • We will support your grant applications: Grant agencies often value support for open standard formats as evidenced by several previous grant evaluations. We will provide detailed support letters that explain your involvement and commitment to disseminate your data. We will also provide statistics of your data usage.

Pathway Commons will avoid duplication of advanced features of source databases. Users are encouraged to explore these features by following hyperlinks from Pathway Commons.


What can I do with this information?

You can freely query available pathway information and answer questions such as:

  • What proteins interact with my favorite protein?
  • What cell signaling or metabolic pathways involve my favorite protein?
  • Is my favorite protein involved in transport events or biochemical reactions?
  • What enzymes use my metabolite of interest as a substrate?

What kind of information is part of each cell signaling and metabolic pathway?

Pathways from different databases are defined by different levels of detail. Details that may be included are proteins, small molecules, DNA, RNA, complexes and their cellular locations, different types of physical interactions, such as molecular interaction, biochemical reaction, catalysis, complex assembly and transport, gene regulation, genetic interactions, post-translational protein modifications, original citations, experimental evidence and links to other databases e.g. of protein sequence annotation. Some information is only available in the downloaded BioPAX files.

How were the pathways collected?

Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction.

How good is the quality of Pathway Commons?

The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons allows users to filter data by various criteria, including data source, which should allow viewing a restricted subset of high quality data. In the future, Pathway Commons will implement published algorithms to automatically assess data quality and allow this as an additional filter.

Computational Biologists

What can I do with this information?

You can download and incorporate this biological pathway data as part of metabolic and gene pathway analysis software in BioPAX Level 3 format. Details about the BioPAX format

How many pathways are part of Pathway Commons?

Please see the statistics page for up to the minute information.

What is cPath2?

cPath2 is an open-source data management software that runs the Pathway Commons web service. You can download it for your own use the developer site.

Can I access Pathway Commons data via a web service

Yes! A web service is available to answer specific queries with computer readable responses for intergration with other network analysis components. This is designed to enable third party software and scripts to easily access the information.

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Kortenhorst M.S.Q., et al. Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors Epigenetics 2013
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Gao J., et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal Science Signaling 2013
Gu Y., et al. Network analysis of genomic alteration profiles reveals co-altered functional modules and driver genes for glioblastoma Molecular BioSystems 2013
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Liu Z., et al. In silico drug repositioning-what we need to know Drug Discovery Today 2013
Mayer M.L., et al. Rescue of dysfunctional autophagy attenuates hyperinflammatory responses from cystic fibrosis cells Journal of Immunology 2013
Kamburov A., et al. The ConsensusPathDB interaction database: 2013 Update Nucleic Acids Research 2013
Zhao M., et al. TSGene: A web resource for tumor suppressor genes Nucleic Acids Research 2013
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Cheng L., et al. Global gene expression and functional network analysis of gastric cancer identify extended pathway maps and GPRC5A as a potential biomarker Cancer Letters 2012
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For questions and feedback, join the mailing list.

Pathway Commons is a collaboration between the Bader Lab at the University of Toronto, the Sander Lab at the cBio Center for Information Biology, Dana-Farber Cancer Institute and the Computational biology collaboratory at Harvard Medical School, and the Demir Lab, Oregon Health & Science University.

Pathway Commons was originally developed at the Memorial Sloan Kettering Cancer Center and the University of Toronto.

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