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Updated: Aug 16, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
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GraphML-SBGN bidirectional converter for metabolic networks.

Irina Balaur1,2, Ludovic Roy1, Vasundra Touré1,3

  • 1European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France.

Journal of Integrative Bioinformatics
|December 23, 2022
PubMed
Summary

This study introduces ySBGN, a converter for biological pathway diagrams. It enables seamless translation between the yEd Graph Editor and the Systems Biology Graphical Notation Markup Language (SBGN-ML) standard.

Keywords:
GraphMLRecon2 human metabolic reconstructionprocess descriptionsystems biology graphical notationsystems biology standard

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Systems biology research requires efficient tools for managing and visualizing large biological networks.
  • Current tools may lack interoperability between general graph editors and standardized biological notation formats.

Purpose of the Study:

  • To develop a bidirectional converter (ySBGN) for translating biological diagrams between yEd Graph Editor (GraphML) and Systems Biology Graphical Notation Markup Language (SBGN-ML).
  • To facilitate the use of powerful general-purpose graph editors for creating and editing complex metabolic pathways in a standardized format.

Main Methods:

  • Development of the ySBGN bidirectional converter software.
  • Utilizing the GraphML format for data exchange with yEd Graph Editor.
  • Employing the Systems Biology Graphical Notation Markup Language (SBGN-ML) as the standard biological format.
  • Testing the converter with the ReconMap resource.

Main Results:

  • The ySBGN converter successfully translates metabolic pathways between yEd Graph Editor (GraphML) and SBGN-ML formats.
  • Demonstrated bidirectional conversion using the ReconMap resource, showcasing tool functionality.
  • Enabled the use of a powerful general-purpose editor for creating standardized biological diagrams.

Conclusions:

  • The ySBGN tool provides a feasible solution for editing and visualizing large biological diagrams in systems biology.
  • It enhances interoperability between general graph editing software and the SBGN standard.
  • Facilitates the creation and standardization of complex metabolic pathway representations.