The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models

Bioinformatics. 2003 Mar 1;19(4):524-31. doi: 10.1093/bioinformatics/btg015.

Abstract

Motivation: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively.

Results: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others.

Availability: The specification of SBML Level 1 is freely available from http://www.sbml.org/

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Database Management Systems
  • Databases, Factual
  • Documentation
  • Gene Expression Regulation / physiology
  • Hypermedia*
  • Information Storage and Retrieval / methods*
  • Metabolism / physiology*
  • Models, Biological*
  • Models, Chemical
  • Programming Languages*
  • Software
  • Software Design
  • Terminology as Topic
  • Vocabulary, Controlled*