Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3

Stuart Moodie, Nicolas Le Novère, Emek Demir, Huaiyu Mi, Alice Villéger

Research output: Contribution to journalArticle

9 Scopus citations

Abstract

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

Original languageEnglish (US)
Pages (from-to)263
Number of pages1
JournalJournal of integrative bioinformatics
Volume12
Issue number2
DOIs
StatePublished - 2015
Externally publishedYes

ASJC Scopus subject areas

  • Medicine(all)

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