Building pathway graphs from BioPAX data in R

N. Benis; D. Schokker; F. Kramer; Mari Smits; M. Suarez-Diez

doi:10.12688/f1000research.9582.2

Building pathway graphs from BioPAX data in R

N. Benis^*, D. Schokker, F. Kramer, Mari Smits, M. Suarez-Diez

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

3 Citations (Scopus)

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.

Original language	English
Article number	2414
Number of pages	13
Journal	F1000 Research
Volume	5
DOIs	https://doi.org/10.12688/f1000research.9582.2
Publication status	Published - 2016

Keywords

BioPAX
Pathways
R
rBiopaxParser

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10.12688/f1000research.9582.2Licence: CC BY

Models of dietary effects on immune responses in pigs (KB-17-003.02-022)
Smits, M.
1/01/13 → 31/12/15
Project: LNV project

Cite this

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title = "Building pathway graphs from BioPAX data in R",

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. ",

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T1 - Building pathway graphs from BioPAX data in R

AU - Benis, N.

AU - Schokker, D.

AU - Kramer, F.

AU - Smits, Mari

AU - Suarez-Diez, M.

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

KW - BioPAX

KW - Pathways

KW - R

KW - rBiopaxParser

U2 - 10.12688/f1000research.9582.2

DO - 10.12688/f1000research.9582.2

M3 - Article

SN - 2046-1402

VL - 5

JO - F1000 Research

JF - F1000 Research

M1 - 2414

ER -

Building pathway graphs from BioPAX data in R

Abstract

Keywords

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Projects

Models of dietary effects on immune responses in pigs (KB-17-003.02-022)

Cite this