The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Abstract

This document defines Version 1 of the Systems Biology Markup Language (SBML) Level 3 Core, an electronic model representation format for systems biology. 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. SBML is defined neutrally with respect to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML, the eXtensible Markup Language (Bray et al., 2004). This document contains many examples of SBML models written in XML. Formal schemas describing the syntax of SBML, as well as other materials and software, are available from the SBML project web site, http://sbml.org/. The SBML project is not an attempt to define a universal language for representing quantitative models. The rapidly evolving views of biological function, coupled with the vigorous rates at which new computational techniques and individual tools are being developed today, are incompatible with a one-size-fits-all idea of a universal language. A more realistic alternative is to acknowledge the diversity of approaches and methods being explored by different software tool developers, and seek a common intermediate format—a lingua franca—enabling communication of the most essential aspects of the models. The definition of the model description language presented here does not specify how programs should communicate or read/write SBML. We assume that for a simulation program to communicate a model encoded in SBML, the program will have to translate its internal data structures to and from SBML, use a suitable transmission medium and protocol, etc., but these issues are outside the scope of this document.

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