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Controlled vocabularies and semantics in systems biology

Lookup NU author(s): Dr Allyson Lister, Dr Matthew Pocock, Professor Darren Wilkinson



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. Molecular Systems Biology 7: 543; published online 25 October 2011; doi:10.1038/msb.2011.77

Publication metadata

Author(s): Pocock M; Wilkinson DJ; Lister A; Courtot M; Juty N; Knupfer C; Waltemath D; Zhukova A; Drager A; Dumontier M; Finney A; Golebiewski M; Hastings J; Hoops S; Keating S; Kell DB; Kerrien S; Lawson J; Lu J; Machne R; Mendes P; Rodriguez N; Villeger A; Wimalaratne S; Laibe C; Hucka M; Le Novere N

Publication type: Article

Publication status: Published

Journal: Molecular Systems Biology

Year: 2011

Volume: 7

Pages: 543

Print publication date: 25/10/2011

Date deposited: 16/02/2012

ISSN (electronic): 1744-4292

Publisher: Nature Publishing Group


DOI: 10.1038/msb.2011.77


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Funder referenceFunder name
BB/F010516/1Biotechnology and Biological Sciences Research Council