The web as a distributed biochemical reactor: Semantically enabled metabolic fate prediction

Over the past decade, we have witnessed Semantic Web Technologies in a tremendous range of applications, from representation and integration of knowledge to enable rich, multi-domain queries to automation of computational workflows using a range of Semantic Web Service platforms. By the virtue of its design, the Semantic Automated Discovery and Integration (SADI) framework provides excellent flexibility and facile discoverability and integration of disparate semantic web services. In this manuscript, we shall demonstrate the application of SADI in the design and implementation of a semantically enabled biochemical reactor framework. In this framework, enzymes and reactions are represented as distinct web services with embedded computational cheminformatics and computational chemistry tools for prediction of reaction feasibility and kinetics. We use a standalone client to reason over molecular descriptions and invoke appropriate SADI services in order to create a biochemical model of metabolism. We provide a simple example of metabolic fate prediction for benzene to demonstrate that this unique modelling framework can provide customizable dynamic and static models of metabolism.