Systems biology graphical notation: process description language Level 1 Version 2.0

Date
2019
Authors
Advisor
Supervisor
Co-Advisor
Co-Supervisor
Instructor
Source Title
Journal of Integrative Bioinformatics
Print ISSN
Electronic ISSN
1613-4516
Publisher
De Gruyter
Volume
16
Issue
2
Pages
20190022
Language
English
Journal Title
Journal ISSN
Volume Title
Series
Abstract

The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).

Course
Other identifiers
Book Title
Citation
Published Version (Please cite this version)