Building pathway graphs from BioPAX data in R

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...

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Detalles Bibliográficos
Autores principales: Benis, Nirupama, Schokker, Dirkjan, Kramer, Frank, Smits, Mari A., Suarez-Diez, Maria
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000Research 2016
Materias:
Software Tool Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5130076/
https://www.ncbi.nlm.nih.gov/pubmed/27990265
http://dx.doi.org/10.12688/f1000research.9582.2
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author Benis, Nirupama
Schokker, Dirkjan
Kramer, Frank
Smits, Mari A.
Suarez-Diez, Maria
author_facet Benis, Nirupama
Schokker, Dirkjan
Kramer, Frank
Smits, Mari A.
Suarez-Diez, Maria
author_sort Benis, Nirupama
collection PubMed
description 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.
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spelling pubmed-51300762016-12-16 Building pathway graphs from BioPAX data in R Benis, Nirupama Schokker, Dirkjan Kramer, Frank Smits, Mari A. Suarez-Diez, Maria F1000Res Software Tool Article 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. F1000Research 2016-12-12 /pmc/articles/PMC5130076/ /pubmed/27990265 http://dx.doi.org/10.12688/f1000research.9582.2 Text en Copyright: © 2016 Benis N et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Benis, Nirupama
Schokker, Dirkjan
Kramer, Frank
Smits, Mari A.
Suarez-Diez, Maria
Building pathway graphs from BioPAX data in R
title Building pathway graphs from BioPAX data in R
title_full Building pathway graphs from BioPAX data in R
title_fullStr Building pathway graphs from BioPAX data in R
title_full_unstemmed Building pathway graphs from BioPAX data in R
title_short Building pathway graphs from BioPAX data in R
title_sort building pathway graphs from biopax data in r
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5130076/
https://www.ncbi.nlm.nih.gov/pubmed/27990265
http://dx.doi.org/10.12688/f1000research.9582.2
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