GraphML-SBGN bidirectional converter for metabolic networks

Irina Balaur; Ludovic Roy; Vasundra Touré; Alexander Mazein; Charles Auffray

doi:10.1515/jib-2022-0030

GraphML-SBGN bidirectional converter for metabolic networks

Irina Balaur, Ludovic Roy, Vasundra Touré, Alexander Mazein, Charles Auffray

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

1 Citation (Scopus)

Abstract

Systems biology researchers need feasible solutions for editing and visualisation of large biological diagrams. Here, we present the ySBGN bidirectional converter that translates metabolic pathways, developed in the general-purpose yEd Graph Editor (using the GraphML format) into the Systems Biology Graphical Notation Markup Language (SBGN-ML) standard format and vice versa. We illustrate the functionality of this converter by applying it to the translation of the ReconMap resource (available in the SBGN-ML format) to the yEd-specific GraphML and back. The ySBGN tool makes possible to draw extensive metabolic diagrams in a powerful general-purpose graph editor while providing results in the standard SBGN format.

Original language	English
Journal	Journal of integrative bioinformatics
Volume	19
Issue number	4
DOIs	https://doi.org/10.1515/jib-2022-0030
Publication status	Published - 1 Dec 2022
Externally published	Yes

Keywords

GraphML
process description
Recon2 human metabolic reconstruction
systems biology graphical notation
systems biology standard

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10.1515/jib-2022-0030

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title = "GraphML-SBGN bidirectional converter for metabolic networks",

abstract = "Systems biology researchers need feasible solutions for editing and visualisation of large biological diagrams. Here, we present the ySBGN bidirectional converter that translates metabolic pathways, developed in the general-purpose yEd Graph Editor (using the GraphML format) into the Systems Biology Graphical Notation Markup Language (SBGN-ML) standard format and vice versa. We illustrate the functionality of this converter by applying it to the translation of the ReconMap resource (available in the SBGN-ML format) to the yEd-specific GraphML and back. The ySBGN tool makes possible to draw extensive metabolic diagrams in a powerful general-purpose graph editor while providing results in the standard SBGN format.",

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AU - Balaur, Irina

AU - Roy, Ludovic

AU - Touré, Vasundra

AU - Mazein, Alexander

AU - Auffray, Charles

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AB - Systems biology researchers need feasible solutions for editing and visualisation of large biological diagrams. Here, we present the ySBGN bidirectional converter that translates metabolic pathways, developed in the general-purpose yEd Graph Editor (using the GraphML format) into the Systems Biology Graphical Notation Markup Language (SBGN-ML) standard format and vice versa. We illustrate the functionality of this converter by applying it to the translation of the ReconMap resource (available in the SBGN-ML format) to the yEd-specific GraphML and back. The ySBGN tool makes possible to draw extensive metabolic diagrams in a powerful general-purpose graph editor while providing results in the standard SBGN format.

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GraphML-SBGN bidirectional converter for metabolic networks

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Keywords

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