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Systems biology graphical notation markup language (SBGNML) version 0.3
Frank T Bergmann1, Tobias Czauderna2, Ugur Dogrusoz3,4
1BioQUANT/COS, Heidelberg University, INF 267, Heidelberg, 69120, Germany.
Journal of Integrative Bioinformatics
|June 23, 2020
Summary
This document updates Systems Biology Graphical Notation (SBGN) to Version 0.3 Markup Language (ML), enhancing biological network visualization and data exchange. The new version improves metadata, map handling, and annotations for broader bioinformatics tool adoption.
Area of Science:
- Systems Biology
- Bioinformatics
- Computational Biology
Background:
- Systems Biology Graphical Notation (SBGN) provides a standardized visual language for biochemical interactions.
- Existing SBGN versions facilitate representation, visualization, and exchange of biological knowledge.
- There is a need for improved metadata, map management, and annotation capabilities in biological network representations.
Purpose of the Study:
- To define Version 0.3 Markup Language (ML) support for the Systems Biology Graphical Notation (SBGN).
- To enhance the representation, visualization, and exchange of biological network data.
- To increase the adoption of SBGN in bioinformatics tools for precise biological knowledge visualization.
Main Methods:
- Development and definition of Version 0.3 Markup Language (ML) for SBGN.
- Incorporation of new attributes for metadata specification.
- Implementation of support for multiple maps, sub-maps, colors, and annotations.
Main Results:
- Version 0.3 ML for SBGN is defined, supporting enhanced graphical notation for biological networks.
- New features include improved metadata handling, multi-map support, and richer annotations.
- Enhanced data exchange capabilities with other systems biology formats like BioPAX and SBML are enabled.
Conclusions:
- Version 0.3 of SBGN Markup Language offers significant improvements for biological network representation and data sharing.
- The enhanced features facilitate more efficient and unambiguous visualization and exchange of complex biological information.
- This update aims to promote wider integration of SBGN into bioinformatics tools, benefiting researchers in systems biology.
Keywords:
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