Pathway Commons version 12 is now online

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Jeffrey Wong

Nov 5, 2019, 12:42:34 PM11/5/19
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Version 12 of Pathway Commons is now online!


Pathway Commons collects and integrates pathway and interaction data from public databases.

**Over 5 700 pathways -- Over 2.4 million interactions -- 22 data sources**

Access this data via web apps, data downloads, web services and software tools designed for experimental biologists, computational biologists and software developers.

Read all about it: Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Research, 24 October 2019. (


Web Apps: ‘Search’ ( pathways by keyword or enter  a gene list and access apps to view binary interactions and perform pathway enrichment analysis. Interactions also available via ‘PCViz’ ( 

Data: Obtain integrated and normalized data from individual data providers or altogether. File downloads ( are available in Biological Pathway Exchange (BioPAX), simple interaction format (SIF) and gene set database (GMT) formats. Web services ( include full-text search and retrieval in the same formats as downloads in addition to systems biology graphical notation (SBGN) and Javascript Object Notation for Linked Data (JSON-LD). SIF web services ( provide rapid graph-theoretical queries of a binary interaction network.


Tools: Access Pathway Commons from Cytoscape using the CyPath2 app ( or from R via paxtoolsR ( View and edit pathways in BioPAX using the Chisio BioPax Editor (ChiBE). Validate BioPAX data using the Paxtools (Java BioPAX toolbox) library ( 

Training: Visit our Pathway Guide ( online textbook to access primers and workflows supporting pathway analysis of experimental data.

Join our Google Group (!forum/pathway-commons-help/join) to ask a question, make a suggestion or just to tap into the PC community. 


The Pathway Commons Team


GitHub (

Twitter (@PathwayCommons)

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