Pathway Commons version 11 is now online
Jeffrey Wong
Version 11 of Pathway Commons is now online!
Pathway Commons collects and integrates pathway and interaction data from public databases.
**Over 4 700 pathways -- Over 2.3 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: ‘Search’ (http://apps.pathwaycommons.org/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’ (http://www.pathwaycommons.org/pcviz/).
Data: Obtain integrated and normalized data from individual data providers or altogether. File downloads (http://www.pathwaycommons.org/pc2/downloads) are available in Biological Pathway Exchange (BioPAX), simple interaction format (SIF) and gene set database (GMT) formats. Web services (http://www.pathwaycommons.org/pc2/) 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 (http://www.pathwaycommons.org/sifgraph/) provide rapid graph-theoretical queries of a binary interaction network.
Tools: Access Pathway Commons from Cytoscape using the CyPath2 app (http://apps.cytoscape.org/apps/cypath2) or from R via paxtoolsR (http://bioconductor.org/packages/release/bioc/html/paxtoolsr.html). View and edit pathways in BioPAX using the Chisio BioPax Editor (ChiBE). Validate BioPAX data using the Paxtools (Java BioPAX toolbox) library (https://github.com/BioPAX/validator).
Training: Visit our Pathway Guide (http://www.pathwaycommons.org/guide/) online textbook to access primers and workflows supporting pathway analysis of experimental data.
Join our Google Group (groups.google.com/forum/#!forum/pathway-commons-help/join) to ask a question, make a suggestion or just to tap into the PC community.
The Pathway Commons Team
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GitHub (github.com/PathwayCommons/)
Twitter (@PathwayCommons)
