Semantic markup languages such as RDF (resource description framework) and OWL (Web ontology language) are increasingly used to externalize metadata or ontology about business data, software, and services in a declarative form. Such externalized descriptions in ontological format are utilized for purposes ranging from search and retrieval to information integration and to business transformation. Ontology can significantly reduce the costs and improve the qualities of deploying, querying, integrating, and transforming enterprise systems. This chapter presents an innovative application of ontology to a model-driven approach to business analysis and transformation. The approach employs a daisy chain of business models for causality analyses. It links, by using semantic models, business processes and business components to IT solutions and capabilities at different phases of business transformation. The semantic models help infer causality of any business pain points and recommend appropriate solutions to fix business or IT shortfalls associated with the pain points in the process of business transformation. In addition, this chapter presents an enterprise-scale ontology management system which provides functionality, scalability, and performance demanded by enterprise applications such as the proposed model-driven business transformation. It describes the design and implementation of the management system which programmatically supports the ontology needs of business applications in a similar to that in which a database management system supports their data needs.