This paper describes the main elements of a functional platform for building Semantic Web Applications, the Semantic Directory (additional information can be found at http://khaos.uma.es/SD-Core). A Semantic Directory provides a resource directory, in which web resources are registered and their semantics published. Using the Semantic Directories we provide a solution for publishing the semantics of resources, and interoperating them with some other applications in the same or different domains. The main idea behind this proposal is to help developers build Semantic Web applications by providing them with functional components for this task. This paper also describes some applications that have been developed using an SD-Core extension: SD-Data. Then, we describe the instantiation of the Khaos Ontology-based Mediation Framework (KOMF) in the Systems Biology domain. This framework provides an architecture that enables the research on the development of ontology-based mediators. Thus, an ontology-based mediator has been produced that has demonstrated its utility in two applications developed in the Amine System Project using the SD-Data for registering semantics: AMMO-Prot and SBMM Assistant. The use of ontologies is limited in the current version of the mediator, but its development as a framework enables the implementation of improvements based on the use of reasoning.