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 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 allows the user to build graphs of entire pathways, including regulated as well as non-regulated elements, and therefore provides amaximum of information. This function is available as part of the rBiopaxParser distribution from Bioconductor.
Highlights
Biological pathways represent signalling 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 signalling pathways
In this paper we describe detailed information on this function which, we believe, will help rBiopaxParser users to better understand the graphs generated from pathway information
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. The new version of the manuscript describes in more detail the differences between the existing function and the new function added to the package. The information gained with the new function is illustrated with biologically relevant material.
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