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

Hasan Balci; Adrien Rougny; Rupert Overall; Irina Balaur; Michael L Blinov; Hanna Borlinghaus; Emek Demir; Andreas Dräger; Robin Haw; Alexander Mazein; Huaiyu Mi; Stuart Moodie; Falk Schreiber; Anatoly Sorokin; Vasundra Touré; Alice Villéger; Tobias Czauderna; Ugur Dogrusoz; Augustin Luna

doi:10.1515/jib-2025-0018

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

J Integr Bioinform. 2026 Jan 23. doi: 10.1515/jib-2025-0018. Online ahead of print.

Authors

Hasan Balci¹, Adrien Rougny², Rupert Overall³, Irina Balaur², Michael L Blinov⁴, Hanna Borlinghaus⁵, Emek Demir^{6

7}, Andreas Dräger^{8

9

10}, Robin Haw¹¹, Alexander Mazein², Huaiyu Mi¹², Stuart Moodie¹³, Falk Schreiber^{5

14}, Anatoly Sorokin¹⁵, Vasundra Touré¹⁶, Alice Villéger¹⁷, Tobias Czauderna¹⁸, Ugur Dogrusoz^{19

20}, Augustin Luna^{1

21}

Affiliations

¹ Computational Biology Branch, 10952 National Library of Medicine , NIH, Bethesda, MD, 20892, USA.
² Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Esch-sur-Alzette, Luxembourg.
³ Humboldt University, Berlin, Germany.
⁴ Center for Cell Analysis and Modeling, UConn Health, Farmington, USA.
⁵ Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.
⁶ Computational Biology Program, Oregon Health & Science University, Portland, OR, USA.
⁷ Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA.
⁸ Data Analytics and Bioinformatics, Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany.
⁹ Quantitative Biology Center (QBiC), Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Ottfried-Müller-Str. 37, 72076 Tübingen, Germany.
¹⁰ German Center for Infection Research (DZIF), Partner Site, Tübingen, Germany.
¹¹ Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada.
¹² Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
¹³ Novo Nordisk A/S, Research and Early Development, Novo Nordisk Park 1, 2760, Måløv, Denmark.
¹⁴ Faculty of Information Technology, Monash University, Melbourne, Australia.
¹⁵ Biological Systems Unit, Okinawa Institute of Science and Technology, Okinawa, Japan.
¹⁶ Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
¹⁷ Freelance IT Consultant, Brighton, UK.
¹⁸ Faculty of Applied Computer Sciences and Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany.
¹⁹ Computer Engineering Department, Bilkent University, Ankara, 06800, Türkiye.
²⁰ i-Vis Research Lab, Bilkent University, Ankara, 06800, Türkiye.
²¹ Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.

PMID: 41569652
DOI: 10.1515/jib-2025-0018

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.

Keywords: SBGN; biological network; circuit diagram; standard; systems biology; visualisation.