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

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
Keywords : R Python
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Contributor : Florence GONDRET Connect in order to contact the contributor
Submitted on : Thursday, January 6, 2022 - 9:56:23 AM
Last modification on : Friday, August 5, 2022 - 2:54:52 PM
Long-term archiving on: : Thursday, April 7, 2022 - 6:38:43 PM


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François Moreews, Hugo Simon, Anne Siegel, Florence Gondret, Emmanuelle Becker. PAX2GRAPHML: a Python library for large-scale regulation network analysis using BIOPAX. Bioinformatics, 2021, 37 (24), pp.4889-4891. ⟨10.1093/bioinformatics/btab441⟩. ⟨hal-03265223⟩



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