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OntoKin: An Ontology for Chemical Kinetic Reaction Mechanisms.

Accepted version
Peer-reviewed

Type

Article

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Authors

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.

Description

Keywords

Kinetics, Models, Chemical, Semantics, Software

Journal Title

J Chem Inf Model

Conference Name

Journal ISSN

1549-9596
1549-960X

Volume Title

60

Publisher

American Chemical Society (ACS)

Rights

All rights reserved
Sponsorship
National Research Foundation Singapore (via Cambridge Centre for Advanced Research and Education in Singapore (CARES)) (unknown)
European Commission Horizon 2020 (H2020) Industrial Leadership (IL) (646121)
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