News: Pathway Commons 2 - Search And Visualize Public Biological Pathway Information. Single Point Of Access.
gravatar for B. Arman Aksoy
6.9 years ago by
B. Arman Aksoy1.2k
New York, NY
B. Arman Aksoy1.2k wrote:

A completely new version of Pathway Commons is now available at

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
  • 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

Also for computational biologists and software developers:

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Pathway Commons web site

The Pathway Commons Team

api news cytoscape • 3.4k views
ADD COMMENTlink modified 6.9 years ago • written 6.9 years ago by B. Arman Aksoy1.2k

any publication ?! how can one cite this ?

ADD REPLYlink written 6.9 years ago by User 1933340

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:

ADD REPLYlink written 6.9 years ago by B. Arman Aksoy1.2k

Hi, Pathway Commons is a great database for gene associations. I have a simple question: can I extract interactions supported by experimental data? Thanks!

ADD REPLYlink written 2.8 years ago by niuyw30
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