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PAX2GRAPHML: a Python library for large-scale regulation network analysis using BIOPAX

Authors
  • Moreews, François
  • Simon, Hugo
  • Siegel, Anne
  • Gondret, Florence
  • Becker, Emmanuelle
Publication Date
Jan 01, 2021
Identifiers
DOI: 10.1093/bioinformatics/btab441
OAI: oai:HAL:hal-03265223v1
Source
HAL
Keywords
Language
English
License
Unknown
External links

Abstract

PAX2GRAPHML is an open source Python library that allows to easily manipulate BioPAX source files as regulated reaction graphs described in .graphml format. 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 allows generating graphs of regulated reactions from a single BioPAX source or by combining and filtering BioPAX sources. Supported by the graph exchange format .graphml, the large-scale 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

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