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Rougny A, Touré V, Albanese J, Waltemath D, Shirshov D, Sorokin A, Bader GD, Blinov ML, Mazein A. SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. Brief Bioinform 2021; 22:6184415. [PMID: 33758926 PMCID: PMC8425392 DOI: 10.1093/bib/bbab049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/13/2021] [Indexed: 11/14/2022] Open
Abstract
A comprehensible representation of a molecular network is key to communicating and understanding scientific results in systems biology. The Systems Biology Graphical Notation (SBGN) has emerged as the main standard to represent such networks graphically. It has been implemented by different software tools, and is now largely used to communicate maps in scientific publications. However, learning the standard, and using it to build large maps, can be tedious. Moreover, SBGN maps are not grounded on a formal semantic layer and therefore do not enable formal analysis. Here, we introduce a new set of patterns representing recurring concepts encountered in molecular networks, called SBGN bricks. The bricks are structured in a new ontology, the Bricks Ontology (BKO), to define clear semantics for each of the biological concepts they represent. We show the usefulness of the bricks and BKO for both the template-based construction and the semantic annotation of molecular networks. The SBGN bricks and BKO can be freely explored and downloaded at sbgnbricks.org.
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Affiliation(s)
- Adrien Rougny
- Corresponding authors: Adrien Rougny, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan and Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Aomi, Tokyo, Japan; E-mail: ; Michael L. Blinov, R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA; E-mail: ; Alexander Mazein, European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France; Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, Pushchino, Moscow Region, 142290, Russia; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg; E-mail:
| | - Vasundra Touré
- Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget, 7491 Trondheim, Norway
| | - John Albanese
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Dagmar Waltemath
- Medical Informatics Laboratory, Institute for Community Medicine, University Medicine Greifswald, D-17475 Greifswald, Germany
| | - Denis Shirshov
- European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France
- Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, Pushchino, Moscow Region, 142290, Russia
| | - Anatoly Sorokin
- Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, Pushchino, Moscow Region, 142290, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky per., Dolgoprudny, Moscow Region, 141700, Russia
- University of Liverpool, Liverpool L7 3EA, UK
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, M5S 3E1, Toronto, Canada
| | - Michael L Blinov
- Corresponding authors: Adrien Rougny, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan and Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Aomi, Tokyo, Japan; E-mail: ; Michael L. Blinov, R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA; E-mail: ; Alexander Mazein, European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France; Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, Pushchino, Moscow Region, 142290, Russia; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg; E-mail:
| | - Alexander Mazein
- Corresponding authors: Adrien Rougny, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan and Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Aomi, Tokyo, Japan; E-mail: ; Michael L. Blinov, R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA; E-mail: ; Alexander Mazein, European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France; Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, Pushchino, Moscow Region, 142290, Russia; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg; E-mail:
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