Informatics infrastructure plays a crucial role in supporting different decision making activities related to pharmaceutical product development, pilot plant and commercial scale manufacturing by streamlining information gathering, data integration, model development and managing all these for easy and timely access and reuse. The foundation of such an infrastructure is the explicitly and formally modeled information. This foundation enables knowledge in different forms, and best manufacturing practices, to be modeled and captured into tools to support the product lifecycle management. This paper discusses the development of ontologies, Semantic Web infrastructure and Web related technologies that make such an infrastructure development possible. While many of the issues addressed in this paper are applicable to a wide spectrum of molecular-based products, we focus our work on the development of pharmaceutical informatics to support Active Pharmaceutical Ingredient (API) as well as drug product development as case studies to illustrate the various aspects of this infrastructure.(c) 2006 Elsevier Ltd. All rights reserved.