Biodiversity 5 min

PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX

PAX2GRAPHML is an open-source Python library that allows to easily manipulate BioPAX source files as regulated reaction graphs described in.graphml format.

Published on 08 February 2022

illustration PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX
© François Moreews

The concept of regulated reactions, which allows connecting regulatory, signaling and metabolic levels, has been used. Biochemical reactions and regulatory interactions are homogeneously described by regulated reactions involving substrates, products, activators and inhibitors as elements.
PAX2GRAPHML is highly flexible and makes it possible to generate graphs of regulated reactions from a single BioPAX source or by combining and filtering BioPAX sources.

 

Example of reaction graph manipulated by PAX2GRAPHML showing reactions and entities as nodes – ©François Moreews

 Supported by the graph exchange format .graphml, the largescale graphs produced from one or more data sources can be further analyzed with PAX2GRAPHML or standard Python and R graph libraries.
Availability and implementation: https://pax2graphml.genouest.org.

 

Reference
François Moreews, Hugo Simon, Anne Siegel, Florence Gondret, Emmanuelle Becker, PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX, 2021; Bioinformatics, 37 (24): 4889-4891. https://doi.org/10.1093/bioinformatics/btab441

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François Moreews Physiology, Environment, and Genetics for the Animal and Livestock Systems

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