Controlled vocabularies and semantics in systems biology.

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TitleControlled vocabularies and semantics in systems biology.
Publication TypeJournal Article
Year of Publication2011
AuthorsCourtot, M, Juty, N, Knüpfer, C, Waltemath, D, Zhukova, A, Dräger, A, Dumontier, M, Finney, A, Golebiewski, M, Hastings, J, Hoops, S, Keating, S, Kell, DB, Kerrien, S, Lawson, J, Lister, A, Lu, J, Machne, R, Mendes, P, Pocock, M, Rodriguez, N, Villeger, A, Wilkinson, DJ, Wimalaratne, S, Laibe, C, Hucka, M, Le Novère, N
JournalMol Syst Biol
Volume7
Pagination543
Date Published2011
ISSN1744-4292
KeywordsAlgorithms, Computational Biology, Computer Simulation, Information Storage and Retrieval, Models, Biological, Semantics, Systems Biology, Vocabulary, Controlled
Abstract

<p>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.</p>

DOI10.1038/msb.2011.77
Alternate JournalMol. Syst. Biol.
PubMed ID22027554
PubMed Central IDPMC3261705
Grant ListBB/F010516/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
R01 GM070923 / GM / NIGMS NIH HHS / United States