Building pathway graphs from BioPAX data in R [version 1; referees: 1 approved, 2 approved with reservations]

Abstract

Biological pathways are increasingly available in the BioPAX format which uses an RDF model for data storage. We can retrieve the information in this data model in the scripting language R using the package rBiopaxParser, which converts the BioPAX format to one readable in R. It also has a function to build a regulatory network from the pathway information, here we describe an extension of this function. The new function will also include non-regulatory interactions in the pathway and thus allow extraction of maximum information. This function will be available as part of the rBiopaxParser distribution from Bioconductor.

Keywords

• Bioinformatics