• JoCIaM-60-108-120

OntoKin: An Ontology for Chemical Kinetic Reaction Mechanisms

Reference: Journal of Chemical Information and Modeling 60(1), 108-120, (2020)

  • The OntoKin ontology has been developed to represent chemical kinetic mechanisms.
  • An ABox Manager has been developed to convert mechanisms from CHEMKIN format to OWL.
  • A Knowledge Base including representations of mechanisms using OWL has been created.

Graphical abstract An ontology for capturing both data and the semantics of chemical kinetic reaction mechanisms has been developed. Such mechanisms can be applied to simulate and understand the behavior of chemical processes, for example, the emission of pollutants from internal combustion engines. An ontology development methodology was used to produce the semantic model of the mechanisms, and a tool was developed to automate the assertion process. As part of the development methodology, the ontology is formally represented using a web ontology language (OWL), assessed by domain experts, and validated by applying a reasoning tool. The resulting ontology, termed OntoKin, has been used to represent example mechanisms from the literature. OntoKin and its instantiations are integrated to create a knowledge base (KB), which is deployed using the RDF4J triple store. The use of the OntoKin ontology and the KB is demonstrated for three use cases - querying across mechanisms, modeling atmospheric pollution dispersion, and as a mechanism browser tool. As part of the query use case, the OntoKin tools have been applied by a chemist to identify variations in the rate of a prompt NOx formation reaction in the combustion of ammonia as represented by four mechanisms in the literature.

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*Corresponding author:
Telephone: +44 (0)1223 762784 (Dept) 769010 (CHU)
Address: Department of Chemical Engineering and Biotechnology
University of Cambridge
West Cambridge Site
Philippa Fawcett Drive
Cambridge CB3 0AS
United Kingdom
Website: Personal Homepage