OntoKin: An Ontology for Chemical Kinetic Reaction Mechanisms

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 NO formation reaction in the combustion of ammonia as represented by four mechanisms in the literature.