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

• Main Authors: Hucka Michael, Bergmann Frank T., Dräger Andreas, Hoops Stefan, Keating Sarah M., Le Novère Nicolas, Myers Chris J., Olivier Brett G., Sahle Sven, Schaff James C., Smith Lucian P., Waltemath Dagmar, Wilkinson Darren J.
• Format: Article
• Language: English
• Published: De Gruyter 2018-03-01
• Series: Journal of Integrative Bioinformatics
• Subjects: sbml; modeling; computational biology; systems biology; standards
• Online Access: https://doi.org/10.1515/jib-2017-0081

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/.