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Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.

Adrien Rougny^1,2, Vasundra Touré³, Stuart Moodie⁴

¹Biotechnology Research Institute for Drug Discovery, AIST, Tokyo135-0064, Japan.

Journal of Integrative Bioinformatics

|June 15, 2019

Summary

This summary is machine-generated.

The Systems Biology Graphical Notation (SBGN) standardizes biological pathway visualization. This update refines the Process Description language (PD) with new glyphs and clarifications for better knowledge exchange.

Keywords:

SBGN biological network circuit diagram standard systems biology visualisation

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Area of Science:

Systems Biology
Bioinformatics
Computational Biology

Background:

Standardized visualization of biological pathways is crucial for knowledge exchange.
The Systems Biology Graphical Notation (SBGN) provides a common language for representing biological networks.
SBGN includes Entity Relationship, Activity Flow, and Process Description (PD) languages.

Purpose of the Study:

To detail Level 1 Version 2.0 of the SBGN Process Description (PD) specification.
To introduce improvements for enhanced precision and clarity in biological knowledge representation.
To support efficient and accurate exchange of biological information across diverse communities.

Main Methods:

The study details the SBGN Process Description (PD) language specification.
It focuses on graphical notation for mechanistic and temporal dependencies in biological systems.
Improvements include new glyphs and clarifications to existing elements.

Main Results:

The updated PD specification (Level 1 Version 2.0) incorporates new glyphs: equivalence operator, subunit, and annotation.
Modifications were made to the usage of submaps for better structural representation.
Clarifications were provided for glyphs such as multimer, empty set, and state variable.

Conclusions:

The enhanced SBGN PD specification improves the precision and expressiveness of biological pathway visualization.
These updates facilitate more accurate and efficient communication of complex biological information.
The standardized notation supports broader accessibility and integration of systems biology data.