SBML Specifications

Levels in SBML are used to manage complexity and evolution of the standard. A Level in SBML is an attempt to provide a given set of features for describing models, with higher Levels providing more powerful features. Within a given SBML Level, minor revisions to SBML are termed Versions and constitute changes within a Level to correct, adjust and refine features. Additionally, to cope with occasional minor editorial changes that may be needed, SBML specification come with Release numbers within Versions.

Please inform the SBML Editors of problems and questions. You can use email or the issue trackers noted below.

Depending on the SBML Level, either RELAX NG schemas or XML Schemas are available. However, the schemas only capture the basic syntax of the format. Semantics and correct usage are not captured by the schemas and can only be understood by reading the specification documents.

SBML Level 3

SBML Level 3 is currently the highest Level of SBML. It has an extensible modular architecture consisting of a central set of fixed features (named SBML Level 3 Core) and optional Packages that can augment the Core by extending existing elements, adding new elements, and adjusting the meaning or scope of elements.

SBML Level 3 Version 2 Core

The most recent definition of SBML Level 3 is Version .

Specification
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core
Authors: Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, and Fengkai Zhang.
This is Release 2 of the specification for SBML Level 3 Version 2, made available on 2019-03-29.
How to cite the publication: Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, and Fengkai Zhang (2019). The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. Journal of Integrative Bioinformatics, 16(2), 20190021 BibTeX RIS

Past releases of SBML Level 3 are available from a separate page.

SBML Level 3 Packages

SBML Level 3 Core is best suited to representing reaction-based models. SBML Level 3 Packages extend the Core with constructs suited to other model types, including constraint-based models, reaction-diffusion models, logical network models, rule-based models, and more. A model expressed using SBML Level 3 can declare which packages it uses in order to guide interpretation by software applications. If an application detects the presence of packages that it does not support, it may inform users if it cannot work with the model.

Packages are developed by separate groups apart from the SBML Editors. If you use an SBML Level 3 Package in your software or your work, please cite the publication associated with the package to give credit to the package developers. Citation information is given in the package detail pages, linked below.

Package Nickname Description Status
Arrays arrays Support for expressing arrays of things Draft available
Hierarchical Model Composition comp Supports the creation of models from other complete models or from model fragments Released
Distributions distrib Support for encoding models that sample values from statistical distributions Released
Dynamic Structures dyn Support for creating and destroying entities during a simulation Draft available
Flux Balance Constraints fbc Support for constraint-based (a.k.a. steady-state) models Released
Groups groups A means for grouping elements Released
Layout layout Support for storing the spatial topology of a network diagram; adjunct to the render package Released
Extended MathML math A suite of packages that collectively allow MathML beyond the subset allowed in SBML core Not started
Multistate, Multicomponent and Multicompartment Species multi Object structures for representing entity pools with multiple states and composed of multiple components, and reaction rules involving them Released
Qualitative Models qual Support for models wherein species do not represent quantity of matter & processes are not reactions per se Released
Rendering render Support for defining the graphical symbols and glyphs used in a diagram of the model; adjunct to the layout package Released
Spatial Processes spatial Support for describing processes that involve a spatial component, and describing the geometries involved Draft available

SBML Level 2

The current definition of SBML Level 2 is Version . Unlike Level 3, SBML Level 2 is monolithic and not a modular format. Its structure is similar to SBML Level 3 Core, but there are no packages extending Level 2.

The separate Levels of SBML are intended to coexist – SBML Level 3 does not render Level 2 obsolete. Software tools that cannot support higher levels can keep using lower levels. Level 2-compatible models and software tools still continue to be used today.

Specification
Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Authors: 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, and Darren J. Wilkinson.
This is Release 1 of the specification for SBML Level 2 Version 5, made available on 2015-08-03.
How to cite the publication: 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, and Darren J. Wilkinson. (2015). Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics, 12(2), 271 BibTeX RIS

Past releases of SBML Level 2 are available from a separate page.

SBML Level 1

The current definition of SBML Level 1 is Version .

Specification
Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions
Authors: Michael Hucka, Andrew Finney, Herbert Sauro, and Hamid Bolouri.
This is the specification for SBML Level 1 Version 2, made available on 2003-08-28.
This specification does not have a journal publication associated with it. Suggested citation: Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri. (2001). Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions. Retrieved from COMBINE, http://identifiers.org/combine.specifications/sbml.level-1.version-2 BibTeX RIS

Past releases of SBML Level 1 are available from a separate page.