Systems biology graphical notation: process description language level 1 version 2.1

The Systems Biology Graphical Notation (SBGN) is an international community effort to standardize the visualization of pathways and networks, making them accessible to scientists from diverse fields while facilitating efficient and ac-curate knowledge exchange among research communities, industry, and other stakeholders in systems biology. SBGN consists of three complementary languages - Entity Relationship (ER), Activity Flow (AF), and Process Description (PD) - each addressing biological and biochemical systems at varying levels of detail. PD, closely aligned with the metabolic and regulatory pathways found in biological literature, books, and academic courses, provides well-defined semantics for precisely representing biological information. The PD language uses a graph structure to represent mechanistic and temporal relationships of biological interactions and transformations. It incorporates distinct node types, including entity pools (e.g., metabolites, proteins, genes, and complexes) and processes (e.g., reactions and associations), with edges representing the connections between nodes (e.g., consumption, production, stimulation, and inhibition). This document details Level 1 Version 2.1 of the PD specification, including several improvements over the previous version (Level 1 Version 2.0): 1) refinements to document structure and terminology, 2) clarifications and updates to specification content, and 3) updated figures and rules.

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Publication Details

Journal
Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
Published
2026-01-22
DOI
https://doi.org/10.1515/jib-2025-0018
Primary Topic
Microbial Metabolic Engineering and Bioproduction
Type
article
Field-Weighted Citation Impact
0.00

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article

Systems biology graphical notation: process description language level 1 version 2.1

Uğur Doğrusöz, Hasan BALCI, Anatoly Sorokin, Tobias Czauderna et al.
Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
Microbial Metabolic Engineering and Bioproduction
article

Systems biology graphical notation: process description language level 1 version 2.1

Uğur Doğrusöz, Hasan BALCI, Anatoly Sorokin, Tobias Czauderna, Alexander Mazein, Robin Haw, Rupert W. Overall, Stuart Moodie, Adrien Rougny, Hanna Borlinghaus, Emek Demir, Andreas Dräger, Augustin Luna, Irina Balaur, Huaiyu Mi, Vasundra Touré, Michael L. Blinov, Falk Schreiber, Alice Villéger
article en

Abstract

The Systems Biology Graphical Notation (SBGN) is an international community effort to standardize the visualization of pathways and networks, making them accessible to scientists from diverse fields while facilitating efficient and ac-curate knowledge exchange among research communities, industry, and other stakeholders in systems biology. SBGN consists of three complementary languages - Entity Relationship (ER), Activity Flow (AF), and Process Description (PD) - each addressing biological and biochemical systems at varying levels of detail. PD, closely aligned with the metabolic and regulatory pathways found in biological literature, books, and academic courses, provides well-defined semantics for precisely representing biological information. The PD language uses a graph structure to represent mechanistic and temporal relationships of biological interactions and transformations. It incorporates distinct node types, including entity pools (e.g., metabolites, proteins, genes, and complexes) and processes (e.g., reactions and associations), with edges representing the connections between nodes (e.g., consumption, production, stimulation, and inhibition). This document details Level 1 Version 2.1 of the PD specification, including several improvements over the previous version (Level 1 Version 2.0): 1) refinements to document structure and terminology, 2) clarifications and updates to specification content, and 3) updated figures and rules.

Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
Ontario Institute for Cancer Research (CA), Hochschule Mittweida (DE), University of Southern California (US), Okinawa Institute of Science and Technology Graduate University (JP), Oregon Health & Science University (US), Bilkent University (TR), University of Luxembourg (LU), Novo Nordisk (Denmark) (DK), University of Konstanz (DE), Norwegian University of Science and Technology (NO), United States National Library of Medicine (US), Humboldt-Universität zu Berlin (DE), Occupational Cancer Research Centre (CA), German Center for Infection Research (DE), National Cancer Institute (US), Center for Cancer Research (US), Monash University (AU), Martin Luther University Halle-Wittenberg (DE), University of Brighton (GB), UConn Health (US), University of Tübingen (DE)
Deutsche Forschungsgemeinschaft, National Institutes of Health, U.S. National Library of Medicine
Industry, innovation and infrastructure
Openalex Percentile: Top 80%
Microbial Metabolic Engineering and Bioproduction
DOIOpen Access PDFOpenAlex
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