The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core

Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson

Research output: Contribution to JournalArticle

Abstract

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. 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 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

Original languageEnglish
Pages (from-to)1-182
Number of pages182
JournalJournal of Integrative Bioinformatics
Volume15
Issue number1
DOIs
Publication statusPublished - 9 Mar 2018

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Keywords

  • computational biology
  • modeling
  • SBML
  • standards
  • systems biology

Cite this

Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., ... Wilkinson, D. J. (2018). The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. Journal of Integrative Bioinformatics, 15(1), 1-182. https://doi.org/10.1515/jib-2017-0081