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 Release 2 of Version 1 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. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the format of annotations, the correction of errata and the addition of clarifications. Other materials and software are available from the SBML project website at http://sbml.org/.
Highlights
This document defines Version 1 of the Systems Biology Markup Language (SBML) Level 3 Core, an electronic model representation format for systems biology
SBML borrows an idea from CellML (Hedley et al, 2001), another model definition language with goals similar to SBML’s, and allows an additional attribute to appear on MathML cn elements; the value of this attribute can be used to indicate the unit of measurement to be associated with the number in the content of the cn element
A model must be interpretable without the benefit of Systems Biology Ontology (SBO) labels
Summary
This document defines Version 1 of the Systems Biology Markup Language (SBML) Level 3 Core, an electronic model representation format for systems biology. A low-volume, broadcast-only web forum/mailing list is available where notifications of revisions to the SBML specification, notices of votes on SBML technical issues, and other critical matters are announced This list is https://groups.google.com/d/forum/sbml-announce and anyone may subscribe to it freely. Borrowing concepts from the World Wide Web. Consortium (Jacobs, 2004), we define SBML errata as changes of the following types: (a) formatting changes that do not result in changes to textual content; (b) corrections that do not affect conformance of software implementing support for a given combination of SBML level and version; and (c) corrections that may affect such software conformance, but add no new language features. Announcements of errata, updates to the SBML specification and other major changes are made on the https://groups.google.com/d/forum/sbml-announce web forum and mailing list
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