Building pathway graphs from BioPAX data in R

Nirupama Benis; Dirkjan Schokker; Frank Kramer; Mari A Smits; Maria Suarez-Diez

doi:10.12688/f1000research.9582.2

Building pathway graphs from BioPAX data in R

F1000Res. 2016 Sep 28:5:2414. doi: 10.12688/f1000research.9582.2. eCollection 2016.

Authors

Nirupama Benis¹, Dirkjan Schokker², Frank Kramer³, Mari A Smits⁴, Maria Suarez-Diez⁵

Affiliations

¹ Host Microbe Interactomics, Wageningen University & Research, Wageningen, Netherlands.
² Wageningen Livestock Research, Wageningen University & Research, Wageningen, Netherlands.
³ Department of Medical Statistics, University Medical Center Goettingen, Goettingen, Germany.
⁴ Wageningen Bioveterinary Research, Wageningen University & Research, Wageningen, Netherlands.
⁵ Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands.

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 a maximum of information. This function is available as part of the rBiopaxParser distribution from Bioconductor.

Keywords: BioPAX; R; pathways; rBiopaxParser.

Grants and funding

This work has been financially supported by the Systems Biology Investment Programme of Wageningen University, KB-17-003.02-022. Frank Kramer’s work is funded by the German Ministry of Education and Research (BMBF) grants FKZ01ZX1508 and FKZ031L0024A.