The challenges of managing the information and knowledge involved in pharmaceutical product development in a systematic and reusable, yet user-friendly, manner are very real and substantive. The benefits of managing the mathematical knowledge component in this can, by itself, lead to significant monetary and time savings, because of the reduced cost of interoperability. In the first part of this series, an ontological approach namely, the OntoMODEL conceptual framework that addresses this need has been presented. In this paper, applications of this framework are described, which involve the use of OntoMODEL as an integrated component of model-based decision support processes in the domain of model predictive control, in decision making associated with drug formulation and in drug process validation. OntoMODEL is shown to provide an easy and intuitive approach to analyze controller performance, which allows the user to experiment with various controller configurations with minimum effort. OntoMODEL can also effectively support the multilevel product formulation process involving both experimental results and evaluation of model-based performance indices. Finally, aspects of regulatory compliance that involve evaluation of models are also well-supported. This paper demonstrates that OntoMODEL can effectively serve as the multifunctional platform for mathematical model-based applications in the domain of chemical and pharmaceutical process and product development.