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Copyright: © 2016 Benis N et al. This work is licensed under the Creative Commons Attribution License (https://creativecommons.org/licenses/by/3.0/) (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

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.

Details

Title
Building pathway graphs from BioPAX data in R
Author
Benis Nirupama; Schokker Dirkjan; Kramer, Frank; Smits, Mari A; Suarez-Diez, Maria
University/institution
U.S. National Institutes of Health/National Library of Medicine
Publication year
2016
Publication date
2016
Publisher
Faculty of 1000 Ltd.
e-ISSN
20461402
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
1953318686
Copyright
Copyright: © 2016 Benis N et al. This work is licensed under the Creative Commons Attribution License (https://creativecommons.org/licenses/by/3.0/) (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.