Towards an Ontology of Biomodelling Larisa Soldatova, Qian Gao, and David Gilbert Department of Information Systems and Computing, Brunel University, Uxbridge, UB8 3PH, London, UK. {Larisa.Soldatova,Qian.Gao,David.Gilbert}@brunel.ac.uk http://brunel.ac.uk/siscm/disc/ Abstract. We present a core Ontology of Biomodelling (OBM), which formally defines principle entities of modelling of biological systems, and follows a structural approach for the engineering of biochemical network models. OBM is fully interoperable with relevant resources, e.g. GO, SBML, ChEBI, and the recording of biomodelling knowledge with On- tology of Biomedical investigations (OBI) ensures efficient sharing and re-use of information, reproducibility of developed biomodels, retrieval of information regarding tools, methods, tasks, bio-models and their parts. An initial version of OBM is available at disc.brunel.ac.uk/obm. Keywords: ontology; knowledge representation; systems biology, mod- elling. 1 Introduction We propose an Ontology of Biomodelling (OBM) that enables formally defined description of the key information about the design and analysis of biological models, motivated by the need for interoperability and re-usability of scientific knowledge. OBM is an important element in BioModel Engineering, a structured approach for the engineering of biochemical network models [2], which facilitates the design, construction and analysis of computational models of biological sys- tems. Ontology engineering is a popular solution for integration, interoperability and re-usability of scientific knowledge and is related to several biomodelling ontological resources. Systems Biology Ontology (SBO) 1 is a set of controlled, relational vocabularies of terms commonly used in systems biology, in particu- lar in computational modelling, and informs the development of SBML 2 . The Ontology of Data Mining (OntoDM) enables recording of most essential infor- mation about predictive modelling as a type of data mining [8]. The Ontology of Biomedical investigations (OBI) provides semantic descriptors to report the most essential information about scientific investigations carried out in biomed- ical domains [4]. OBM employs an OBI approach to the reporting of investigations [4], incor- porating all the relevant representations from other resources such as OntoDM 1 http://www.ebi.ac.uk/sbo 2 http://sbml.org