Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions
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Summary: Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.
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Both SBML and CellML support annotation with SBO terms.
“Both SBML and CellML support annotation with SBO terms. SBML elements contain an optional sboTerm attribute [25, 29, 31].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [29]
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Self-citation
- Authors
- Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Smith, L. P., Waltemath, D., & Wilkinson, D. J.
- Affiliations
- California Institute of Technology (US)
- University of California San Diego (US)
- Virginia Tech (US)
- European Bioinformatics Institute (GB)
- Babraham Institute , Cambridge , United Kingdom of Great Britain and Northern Ireland
- University of Utah (US)
- Vrije Universiteit Amsterdam (NL)
- Heidelberg University (DE)
- University of Connecticut (US)
- University of Washington (US)
- University of Rostock (DE)
- Newcastle University (GB)
- Corresponding author
- Hucka, Michael
- ORCID
- Venue
- Journal of Integrative Bioinformatics
- Publisher
- Walter de Gruyter GmbH
- Published
- 2015-06-01
- Volume
- 12
- Issue
- 2
- Pages
- 731-901
- ISSN
- 1432-4385 (ISSN-L)
- 1613-4516
- OpenAlex
- W4241482610
- Cited by
- 16
- References
- 13
- Citations by year
- 2026: 2 · 2024: 3 · 2023: 2 · 2021: 3 · 2019: 1 · 2018: 2 · 2017: 2 · 2012: 1
- FWCI
- 0.58
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics (publishedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- SBML, XML data structure, metabolic pathways, signaling pathways
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