The Pathway Commons team is happy to announce the release of the PaxtoolsR package on Bioconductor. This is an R package that will bring a large repository of literature-curated data to bioinformatic software developers in R. Among its several features, this package will let you easily access interaction information from a number of databases (e.g. Reactome, BIND, BioGRID, HPRD, etc.), filter on the data sources and find the literature associated with a given interaction. The provided vignette outlines common and key tasks such as data visualization, finding paths between entities in the network, ID mapping, and performing enrichment analyses.
We look forward to seeing the software you build on the Pathway Commons infrastructure. To see the current applications of this data and how this data already integrates with tools like Cytoscape, check out our website Pathway Commons (http://www.pathwaycommons.org).
If you are a database developer for pathway or any type of molecular interaction information (e.g. drug-gene, protein-protein, etc.) and are interested in seeing how the Pathway Commons infrastructure could be used in conjunction with your data, please don't hesitate to contact us.
The Pathway Commons team