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Adding Semantics in Kinetics Models of Biochemical Pathways

Journal article published in 2006 by Nicolas Le Novere, Melanie Courtot, Camille Laibe ORCID
This paper is available in a repository.
This paper is available in a repository.

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Abstract

Abstract The need to exchange,and integrate models drove the community,to design common data format such as SBML. However, as important as was the definition of a common syntax, we also need to tackle the semantics of the models. The community recently proposed MIRIAM, the Minimal Information Requested in the Annotation of Models, a set of rules for curating quantitative models,of biological systems. This standard lists the condition an encoded,model,has to meet to fully correspond to its reference description, and describe how to annotate each of its components. The Systems Biology Ontology (SBO) aims to strictly index, define and relate terms used in quantitative model- ling, and by extension quantitative biochemistry. SBO is currently made up of five different vocabularies: quantitative parameters, parti- cipant roles, modelling frameworks, mathematical expressions – that refers to the three previous branches – and events. SBO can be used not only to annotate quantitative models, but also biochemical ex- periements. It is expected,that the adoption of those two semantic layers will favour the reusability of quantitative biochemical descrip- tions, whether parameters or models. 137 http://www.beilstein-institut.de/escec2006/proceedings/LeNovere/LeNovere.pdf ESCEC, March 19,, 2006, R�desheim/Rhein, Germany