Controlled vocabularies and semantics in systems biology
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.
Additional Information© 2011 EMBO and Macmillan Publishers Limited. Molecular Systems Biology is an open-access journal published by European Molecular Biology Organization and Nature Publishing Group. This work is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License. Received 28 March 2011; Accepted 7 September 2011; Published online 25 October 2011. We thank the National Institute of General Medical Sciences, European Commission (FP7 SP4 Capacities Preparatory Phase 211601, ELIXIR) and Marie-Curie BioStar for providing resources to carry out this work.
Published - Courtot2011p16335Mol_Syst_Biol.pdf