Controlled vocabularies and semantics in systems biology

By Mélanie Courtot, N. Juty, Christian Knüpfer, Dagmar Waltemath, A. Zhukova, Andreas Dräger, M. Dumontier, A. Finney, Martin Golebiewski, Janna Hastings and 17 more. Molecular Systems Biology, 2011

326 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8562530c367f43fe355a20f7099c9fd09b5641c7

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In Molecular Biology

Citations in the corpus

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 (2012, background): “Furthermore, recognized semantic terms are required if such models are to be used in computational pipelines, allowing for the automation of the systems biology life cycle, from model generation, through to integration with experimental omics data, and simulation (17).”
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models (2015, methodology): “SBML models are first generated using COBRApy (32), then ModelPolisher inserts MIRIAM annotations and adds specific terms from the Systems Biology Ontology (SBO) (38) to individual model components in order to better point out their role.”