Systems Biology Ontology

Welcome to SBO

The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of seven orthogonal vocabularies defining: the roles of reaction participants (eg. "substrate"), quantitative parameters (eg. "Michaelis constant"), a precise classification of mathematical expressions that describe the system (eg. "mass action rate law"), the modeling framework used (eg. "logical framework"), and a branch each to describe entity (eg. "macromolecule") and interaction (eg. "process") types, and a branch to define the different types of metadata that may be present within a model.

SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. More information about SBO can be found here.

SBO is a project of the BioModels.net effort and is developed through community collaboration.

Publications

• Courtot M., Juty N., Knüpfer C., Waltemath D., Zhukova A., Dräger A., Dumontier M., Finney A., Golebiewski M., Hastings J., Hoops S., Keating S., Kell D.B., Kerrien S., Lawson J., Lister A., Lu J., Machne R., Mendes P., Pocock M., Rodriguez N., Villeger A., Wilkinson D.J., Wimalaratne S., Laibe C., Hucka M., Le Novère N. (2011)

  Controlled vocabularies and semantics in systems biology.

  Molecular Systems Biology, 7:543

  [DOI] [MSB]

• Le Novère N, Courtot M, Laibe C (2007)

  Adding semantics in kinetics models of biochemical pathways.

  Proceedings of the 2nd International Symposium on experimental standard conditions of enzyme characterizations.

  [Proceeding]

• Le Novère N. (2006)

  Model storage, exchange and integration.

  BMC Neuroscience, 7(Suppl 1):S11.

  [Medline] [OpenAccess]

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