Controlled vocabularies and semantics in systems biology

Mélanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, Andreas Dräger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B. Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer MacHne, Pedro Mendes, Matthew PocockNicolas Rodriguez, Alice Villeger, Darren J. Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, Nicolas Le Novère*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

171 Citations (Scopus)

Abstract

The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments.

Original languageEnglish
Article number543
Pages (from-to)1-12
Number of pages12
JournalMolecular Systems Biology
Volume7
Issue number1
DOIs
Publication statusPublished - 1 Jan 2011
Externally publishedYes

Keywords

  • dynamics
  • kinetics
  • model
  • ontology
  • simulation

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