The systems biology graphical notation.
Abstract
Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.
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“Whenever possible and appropriate, it is recommended to follow some sort of standard graphical notation, such as the systems biology graphical notation (SBGN), to facilitate the reader’s comprehension.(36) 2.”
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- Authors
- Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villéger, A., Boyd, S. E., Calzone, L., Courtot, M., Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K., & Kitano, H.
- Affiliations
- California Institute of Technology (US)
- SRI International (US)
- University of Edinburgh (GB)
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE)
- Memorial Sloan Kettering Cancer Center (US)
- University of Hertfordshire (GB)
- National Institutes of Health (US)
- University of Auckland (NZ)
- University of Washington (US)
- Heidelberg University (DE)
- RIKEN (JP)
- European Bioinformatics Institute (GB)
- Systems Biology Institute (JP)
- University of Manchester (GB)
- Monash University (AU)
- Inserm (FR)
- Roslin Institute (GB)
- Keio University (JP)
- Siberian Branch of the Russian Academy of Sciences (RU)
- Bilkent University (TR)
- Ontario Institute for Cancer Research (CA)
- Stellenbosch University (ZA)
- Okinawa Institute of Science and Technology Graduate University (JP)
- ORCID
- Hucka, Michael
- Mi, Huaiyu
- Moodie, Stuart
- Schreiber, Falk
- Sorokin, Anatoly
- Demir, Emek
- Aladjem, Mirit I
- Wimalaratne, Sarala M
- Ghazal, Peter
- Kawaji, Hideya
- Li, Lu
- Calzone, Laurence
- Freeman, Tom C
- Funahashi, Akira
- Ghosh, Samik
- Jouraku, Akiya
- Kim, Sohyoung
- Kolpakov, Fedor
- Luna, Augustin
- Sahle, Sven
- Schmidt, Esther
- Watterson, Steven
- Wu, Guanming
- Goryanin, Igor
- Kell, Douglas B
- Sander, Chris
- Sauro, Herbert
- Snoep, Jacky L
- Kohn, Kurt
- Kitano, Hiroaki
- Venue
- Nature Biotechnology
- Published
- 2009-08
- Volume
- 27
- Issue
- 8
- Pages
- 735-741
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2069157810
- Cited by
- 903
- References
- 34
- Citations by year
- 2026: 20 · 2025: 26 · 2024: 26 · 2023: 42 · 2022: 39 · 2021: 72 · 2020: 47 · 2019: 53 · 2018: 56 · 2017: 50 · 2016: 57 · 2015: 75 · 2014: 53 · 2013: 67 · 2012: 62
- FWCI
- 29.15
- Type
- journal article
- Language
- en
- Update notices
- erratum (2009-09-01)
- Open access
- closed
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- KOPS (University of Konstanz) (submittedVersion)
- Bilkent University Institutional Repository (Bilkent University) (submittedVersion)
- Funders
- National Institutes of Health
- Engineering and Physical Sciences Research Council
- Biotechnology and Biological Sciences Research Council (BB/F010516/1, BBS/E/D/05191131, BB/D019621/1, BB/G530441/1, BB/E016065/1)
- National Cancer Institute
- National Institute of General Medical Sciences (R01GM081070)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- SBGN, graphical notation, visual language, process diagrams, entity relationship diagram, biological network visualization, gene expression regulation, signal transduction, metabolism
- MeSH terms
- Computer Graphics, Software, Internet, Systems Biology, History, 20th Century
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