A completely new version of Pathway Commons is now available at http://www.pathwaycommons.org
Pathway Commons is a collection of publicly available pathways, currently containing 6 pathway and interaction databases, focused on human. These are: Reactome, NCI Pathway Interaction Database, PhosphoSitePlus, HumanCyc, HPRD and PANTHER. We will add more databases in the future.
What’s new? Lots!
- Completely rewritten software system three years in the making.
- Supports metabolism, gene regulation, molecular and genetic interactions, and signaling, including molecular states (e.g. phosphorylation TP53), generic molecules (e.g. Wnt family of proteins) with BioPAX Level 3
- Visualize pathways and networks in your web browser using the new PCViz system. At http://www.pathwaycommons.org/pcviz/
- Download pathways and networks from Pathway Commons in Cytoscape for analysis using the new CyPath2 app for Cytoscape 3
- Pathway viewer and editor linked to Pathway Commons, called ChiBE, at https://code.google.com/p/chibe/
Also for computational biologists and software developers:
- PC2 Web service:
- advanced graph queries
- Normalized and up-to-date data
- Resolvable URIs (http://purl.org/pc2/<version>/*)
- Programmatic access
- Batch downloads at http://www.pathwaycommons.org/pc2/downloads.html
- Linked Data: http://purl.org/pc2/sparql and http://purl.org/pc2/fct
- Standard language for Biological Pathway Exchange and a software library for handling data (BioPAX & Paxtools). http://www.biopax.org/
- Previous Pathway Commons website is still available at http://www.pathwaycommons.org/pc/ However, it is now static.
Send us your feedback at http://www.pathwaycommons.org/pc/get_feedback.do
Follow us on Twitter for updates: http://twitter.com/PathwayCommons
The Pathway Commons Team
any publication ?! how can one cite this ?
Publication on the way; but might take a while to get this one out. In the meantime, please feel free to cite the first Pathway Commons paper:
Hi, Pathway Commons is a great database for gene associations. I have a simple question: can I extract interactions supported by experimental data? Thanks!