Design and development of chemical ontologies for reaction representation

This paper describes the development of chemical ontologies applied to the representation of organic chemical reactions. The ontologies are built using the methodology known as methontology. The hierarchically structured set of terms describing the subdomains, namely, organic reactions, organic compounds, and reagents, are constructed into individual ontologies. The ontologies consist of about 200 concepts and around 125 individuals. A set of binary relations is defined in order to integrate the ontologies with applications. The ontologies are implemented as an XML application with a set of vocabulary describing the domain knowledge. This paper also features an easy-to-use chemical ontological support system (COSS) intended to represent organic chemical reactions automatically. As a model application, the automatic representation of aliphatic nucleophilic substitution reactions is demonstrated using COSS. The paper also describes a keyword-based search system whose functionality is backed with COSS.