Pathway Commons version 12 is now online

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Jeffrey Wong

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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. (https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz946/5606621)

 

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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pathwaycommons.org

GitHub (github.com/PathwayCommons/)

Twitter (@PathwayCommons)

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