Ontologies have become ubiquitous in information systems. They constitute the semantic Web's backbone, facilitate e-commerce, and serve such diverse application fields as bioinformatics and medicine. As ontology development becomes increasingly widespread and collaborative, developers are creating ontologies using different tools and different languages. These ontologies cover unrelated or overlapping domains at different levels of detail and granularity. A uniform framework, which we present here, helps users manage multiple ontologies by leveraging data and algorithms developed for one tool in another. For example, by using an algorithm we developed for structural evaluation of ontology versions, this framework lets developers compare different ontologies and map similarities and differences among them. Multiple-ontology management includes these tasks: maintain ontology libraries, import and reuse ontologies, translate ontologies from one formalism to another, support ontology versioning, specify transformation rules between different ontologies and version, merge ontologies, align and map between ontologies, extract an ontology's self-contained parts, support inference across multiple ontologies, support query across multiple ontologies.