PROTEGE-II is a suite of tools and a methodology for building knowledge-based systems and domain-specific knowledge-acquisition tools. In this paper, we show how PROTEGE-II can be applied to the task of providing protocol-based decision support in the domain of treating HIV-infected patients. To apply PROTEGE-II, (1) we construct a decomposable problem-solving method called episodic skeletal-plan refinement, (2) we build an application ontology that consists of the terms and relations in the domain, and of method-specific distinctions not already captured in the domain terms, and (3) we specify mapping relations that link terms from the application ontology to the domain-independent terms used in the problem-solving method. From the application ontology, we automatically generate a domain-specific knowledge-acquisition tool that is custom-tailored for the application. The knowledge-acquisition tool is used for the creation and maintenance of domain knowledge used by the problem-solving method. The general goal of the PROTEGE-II approach is to produce systems and components that are reusable and easily maintained. This is the rationale for constructing ontologies and problem-solving methods that can be composed from a set of smaller-grained methods and mechanisms. This is also why we tightly couple the knowledge-acquisition tools to the application ontology that specifies the domain terms used in the problem-solving systems. Although our evaluation is still preliminary, for the application task of providing protocol-based decision support, we show that these goals of reusability and easy maintenance can be achieved. We discuss design decisions and the tradeoffs that have to be made in the development of the system.