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sbgntikz-a TikZ library to draw SBGN maps
1Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan.
A new TikZ library, sbgntikz, enables the creation and customization of Systems Biology Graphical Notation (SBGN) maps within LaTeX documents. This tool supports all SBGN languages and includes a converter for SBGN Markup Language files.
Area of Science:
- Systems Biology
- Bioinformatics
- Computational Biology
Background:
- Systems Biology Graphical Notation (SBGN) is the standard for graphical representation of biological maps.
- SBGN includes Process Description, Activity Flow, and Entity Relationship languages.
- TikZ is a popular LaTeX package for creating graphics programmatically.
Purpose of the Study:
- To introduce sbgntikz, a TikZ library for drawing and customizing SBGN maps in LaTeX.
- To provide a tool that integrates SBGN map creation directly into LaTeX documents.
- To facilitate the visualization of complex biological networks.
Main Methods:
- Developed sbgntikz as a TikZ library.
- Implemented support for all glyphs across the three SBGN languages.
- Created a converter for SBGN Markup Language (SBGN-ML) to TikZ.
Main Results:
- sbgntikz allows direct drawing and customization of SBGN maps using TikZ.
- The library supports all SBGN glyphs and complex glyph assemblies.
- A converter transforms SBGN-ML files into TikZ pictures or PDF outputs.
Conclusions:
- sbgntikz simplifies the creation of publication-quality SBGN maps within LaTeX.
- The tool enhances the integration of biological network visualization into scientific documents.
- sbgntikz and its converter are freely available for various operating systems.
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