Building pathway graphs from BioPAX data in R

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

Research output: Contribution to journalArticleAcademicpeer-review

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 languageEnglish
Article number2414
Number of pages13
JournalF1000 Research
Volume5
DOIs
Publication statusPublished - 2016

Fingerprint

Information Services
Information Storage and Retrieval
Language
Data structures
Data storage equipment

Cite this

@article{472bdfe7f70b40fbab5918156f4eea61,
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.",
author = "N. Benis and D. Schokker and F. Kramer and Mari Smits and M. Suarez-Diez",
year = "2016",
doi = "10.12688/f1000research.9582.2",
language = "English",
volume = "5",
journal = "F1000 Research",
issn = "2046-1402",
publisher = "F1000Research",

}

Building pathway graphs from BioPAX data in R. / Benis, N.; Schokker, D.; Kramer, F.; Smits, Mari; Suarez-Diez, M.

In: F1000 Research, Vol. 5, 2414, 2016.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

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.

U2 - 10.12688/f1000research.9582.2

DO - 10.12688/f1000research.9582.2

M3 - Article

VL - 5

JO - F1000 Research

JF - F1000 Research

SN - 2046-1402

M1 - 2414

ER -