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Published on: October 13, 2018
Systems biology graphical notation: process description language level 1 version 2.1
Hasan Balci1, Adrien Rougny2, Rupert Overall3
1Computational Biology Branch, 10952 National Library of Medicine , NIH, Bethesda, MD, 20892, USA.
The Systems Biology Graphical Notation (SBGN) Process Description (PD) language standardizes biological pathway visualization. This updated specification (Level 1 Version 2.1) refines terminology, content, and figures for clearer biological information exchange.
Area of Science:
- Systems Biology
- Bioinformatics
- Computational Biology
Background:
- Standardized visualization is crucial for systems biology knowledge exchange.
- Existing pathway representations lack consistent semantics.
- The Systems Biology Graphical Notation (SBGN) aims to address this standardization gap.
Purpose of the Study:
- To detail the Level 1 Version 2.1 specification of the SBGN Process Description (PD) language.
- To introduce improvements over the previous version (Level 1 Version 2.0).
- To enhance the precision and accessibility of biological pathway and network visualization.
Main Methods:
- The study details the SBGN Process Description (PD) language specification.
- It describes the graph structure, node types (entity pools, processes), and edge types used in PD.
- The document outlines refinements to structure, terminology, content, figures, and rules.
Main Results:
- The document presents Level 1 Version 2.1 of the SBGN PD specification.
- Key improvements include refined terminology, updated content, and revised figures and rules.
- These updates enhance the clarity and accuracy of biological network representation.
Conclusions:
- The updated SBGN PD specification (Level 1 Version 2.1) provides a more robust standard for visualizing biological pathways.
- This standardization facilitates better communication and knowledge exchange in systems biology.
- The refinements ensure precise representation of biological interactions and transformations.
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