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The Systems Biology Graphical Notation: a standardised representation of biological maps
Vasundra Touré1, Alexander Mazein2, Adrien Rougny3,4, Andreas Dräger5,6, Ugur Dogrusoz7, Michael Blinov8, Augustin Luna9
1 Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
2 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
3 Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Aomi, Tokyo 135-0064, Japan
4 Computational Bio Big-Data Open Innovative Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan
5 Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Center for Bioinformatics Tübingen (ZBIT), 72076 Tübingen, Germany
6 Department for Computer Science, University of Tübingen, 72076 Tübingen, Germany
7 Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
8 R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA
9 cBio Center, Dana-Farber Cancer Institute, Boston, MA; Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
Background: Visualization of biological processes plays an essential role in life science research. Over time, diverse forms of diagrammatic representations, akin to circuit diagrams, have evolved without well-defined semantics potentially leading to ambiguous network interpretations and difficult programmatic processing.
Results: The Systems Biology Graphical Notation (SBGN) is a standard developed to reduce ambiguity in the visual representation of biomolecular networks. It provides specific sets of well-defined symbols for various types of biological concepts. SBGN comprises three complementary languages: Process Description (PD), Entity Relationship (ER), and Activity Flow (AF). SBGN PD is based on reactions and is well-suited for detailed sequential biochemical mechanisms, for instance, to represent metabolic pathways. SBGN AF shows cascades of influences between the activities carried by biomolecular entities (e.g., stimulation, inhibition) and is particularly useful when the precise molecular mechanisms are unknown or do not need to be shown, for instance, to represent signalling pathways and regulatory networks. SBGN ER represents independent interactions between features of biological entities, which avoids combinatorial explosions of represented biological states and interactions. The XML-based SBGN Markup Language (SBGN-ML) facilitates convenient storage and exchange of SBGN maps, supported by the library libSBGN.
Discussion: The SBGN project is an ongoing open community-driven effort coordinated and maintained by an elected international editorial board. Annual workshops, GitHub and mailing lists are used as leading discussion platforms. Major research projects, such as the Virtual Metabolic Human, and pathway databases such as Reactome and WikiPathways display their maps following the SBGN guidelines. Furthermore, a wide range of tools supports SBGN. SBGN regularly offers student coding events through the Google Summer of Code program.
Availability: All documents and source code are freely available at http://sbgn.org and https://github.com/sbgn. Contributions are welcome.
Contact: sbgn-discuss@googlegroups.com
Keywords: SBGN, circuit diagram, biological network, visualisation, systems biology
References:
Visualization of biological processes plays an essential role in life science research. Diverse forms of diagrammatic representations, akin to circuit diagrams, have evolved without well-defined semantics potentially leading to ambiguous network interpretations and difficult programmatic processing.
SBGN is a standard developed to reduce ambiguity in the visual representation of biomolecular networks. It provides specific sets of well-defined symbols for various types of biological concepts. SBGN comprises three complementary languages: Process Description (PD), Activity Flow (AF), and Entity-Relationship (ER). PD allows representing the reactions underlying detailed sequential biochemical mechanisms, as found in metabolic pathways. AF is used to describe cascades of influences between activities of biomolecular entities, for which precise molecular mechanisms might not be known or be neglectable, as those of signalling and regulatory networks. ER permits representing independent interactions between features of biological entities, which avoids combinatorial explosions of represented biological states and interactions. SBGN-ML and the library libSBGN facilitate storage and exchange of maps.
SBGN is a community-driven effort coordinated by elected editors. Workshops, GitHub, and mailing lists are leading discussion platforms. Major research projects, databases, and software tools support SBGN.
Documents and source code are freely available at http://sbgn.org and https://github.com/sbgn. Contact: sbgn-discuss@googlegroups.com