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.
Highlights
Biological pathways represent signaling and/or metabolic events involving protein and non-protein molecules
The BioPAX format is being actively developed, with BioPAX level 2 format focusing on metabolic pathways and BioPAX level 3 introducing full support for signaling pathways
It comes with several options that are useful to probe the data and extract specific information from it, for example participants of a pathway, stoichiometric conditions to be fulfilled for an interaction, etc
Summary
1. Lynn Fink, University of Queensland, Diamantina Institute, Woolloongabba, Australia. This article is included in the International Society for Computational Biology Community Journal gateway. This article is included in the RPackage gateway. Any reports and responses or comments on the article can be found at the end of the article
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