title: Building pathway graphs from BioPAX data in R.
abstract: Biological pathways are increasingly available in the BioPAX format which uses an RDF model for data storage. One can retrieve the information in this data model in the scripting language R using the packagerBiopaxParser, 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 allows the user to build graphs of entire pathways, including regulated as well as non-regulated elements, and therefore provides a maximum of information. This function is available as part of therBiopaxParserdistribution from Bioconductor.
authors.affiliation: Host Microbe Interactomics, Wageningen University & Research, Wageningen, Netherlands.
authors.forename: Nirupama
authors.initials: N
authors.lastname: Benis
authors.affiliation: Wageningen Livestock Research, Wageningen University & Research, Wageningen, Netherlands.
authors.forename: Dirkjan
authors.initials: D
authors.lastname: Schokker
authors.affiliation: Department of Medical Statistics, University Medical Center Goettingen, Goettingen, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Kramer
authors.affiliation: Wageningen Bioveterinary Research, Wageningen University & Research, Wageningen, Netherlands.
authors.forename: Mari A
authors.initials: MA
authors.lastname: Smits
authors.affiliation: Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands.
authors.forename: Maria
authors.initials: M
authors.lastname: Suarez-Diez
keywords: BioPAX; R; pathways; rBiopaxParser