Pathway Commons version 9 is now online

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Jeffrey Wong

Jul 21, 2017, 5:46:04 PM7/21/17
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Version 9 of Pathway Commons is now online!

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

**Over 4 000 pathways -- Over 1.3 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.

Web Apps: Find and view pathways with our new Search app by entering a pathway name or gene list. Find and view interactions between one or more genes with 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).

Tools: Access Pathway Commons from Cytoscape using the CyPath2 app or from R via the paxtoolsR package. 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 new Guide online textbook to access case studies, primers, presentations 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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