Pathway Commons v7 is now available!
Pathway Commons is a collection of publicly available pathways, currently containing 18 pathway and interaction databases, focused on human. These are: Reactome, NCI Pathway Interaction Database: Pathway, PhosphoSitePlus, HumanCyc, HPRD, PANTHER Pathway, DIP, BioGRID, IntAct, IntAct complex, BIND, CORUM, CTD, DrugBank, miRTarBase, KEGG Pathway, TRANSFAC, Recon X. We will continue to add more data in the future.
This release adds six new pathway data sources, converted to BioPAX, and includes new versions of Reactome, UniProt, ChEBI, UniChem data. PSI-MI data were converted to BioPAX using the updated converter that does not create hundreds duplicate interactions and participants. We fixed a number of other issues, improved the online documentation and output formats (there are now “HGNC Symbol” versions of the GSEA archives, and the extended SIF files in the batch downloads contain new “PATHWAY_NAMES” column).
PC2 v7 is powered by updated cPath2 software and the latest Paxtools and BioPAX Validator Java libraries. The webservice API is the same as in the previous release (PC2 v6), but one can now use UNDIRECTED as direction parameter value with the graph queries (and this option is now the default for ‘neighborhood’ queries, which now can also return BioPAX MolecularInteraction objects).
Please send us your feedback at pc-...@pathwaycommons.org
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The Pathway Commons Team