Dagmar Köhn, Nicolas Le Novere, and Christian Knüpfer
Beyond Structure: KiSAO and TEDDY - Two Ontologies Addressing Pragmatical and Dynamical Aspects of Computational Models in Systems Biology
Miscellaneous publication, 3rd International Biocuration Conference, Available from Nature Precedings .
Computational models are becoming more and more the central scientiﬁc paradigm for understanding the complexity of living systems. With the increasing number and size of these models there is a growing need for model reuse and exchange. Furthermore, detailed models are not manageable without computer support. There are eﬀorts to formalise the mathematical structure of models (e.g. SBML) and to standardise the kinetic and biological meaning of model components (e.g. SBO, GO, UniProt). However, formalising only the structure of computational models is not suﬃcient to easily exchange and reuse models and to achieve full computer support for modelling. We also need to formalise the pragmatical and dynamical aspects of models. For this purpose we propose two ontologies: The Kinetic Simulation Algorithm Ontology (KiSAO) and the TErminology for the Description of DYnamics (TEDDY). KiSAO covers algorithms used for simulation of computational models. The ontology classiﬁes and puts into context existing simulation algorithms. For the classiﬁcation, it uses several criteria such as deterministic/stochastic or spatial/non-spatial. The aim of TEDDY is to provide terms for describing and characterising dynamical behaviours, observable dynamical phenomena, and control elements of biological models and biological systems in Systems Biology and Synthetic Biology.