Pathway Commons v5 is now available at (see: PC2 web services)

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Igor Rodchenkov

Nov 7, 2014, 4:25:29 PM11/7/14

Pathway Commons is a collection of publicly available pathways, currently containing 12 pathway and interaction databases, focused on human. These are: Reactome, NCI Pathway Interaction Database, PhosphoSitePlus, HumanCyc, HPRD, PANTHER Pathway, DIP, BioGRID, IntAct, IntAct complexes, BIND and CORUM. We will continue to add more databases in the future.

What’s new?  Lots!

  • Data

    • updated existing and added new data sources;

    • developed and applied a new improved converter from PSI to BioPAX format which now considers protein states (experimental forms) and genetic interactions;

    • SIF converter and the output have been changed considerably;

    • a smaller BioPAX archive (‘Detailed_Process_Data’), which contains no data converted from PSI-MI sources, is available to download in addition to ‘All’ and by-source BioPAX archives;

    • PC archives site initiated to maintain old versions (files, not web services)

  • Web Service and Documentation

    • main site polished;

    • web service API is unchanged;

    • CORS support enabled for website developers (let’s test...);

    • a few bugs in graph queries fixed;

    • new look and feel (Twitter Bootstrap);

    • new binary relation types described (SIF format);

  • Logs

    • now counting and reporting the number of unique IP addresses (per file, query, provider, etc.);

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Several interactions from PANTHER Pathway were lost or replaced with a nonequivalent one during the merge into the BioPAX database due to using the same URI for entities of different pathways. This error will be fixed soon in the next PANTHER and Pathway Commons releases.


The Pathway Commons Team

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