To effectively use ontologies on the Web, it is essential that changes in ontologies are managed well. This paper analyzes the topic of ontology versioning in the context of the Web by looking at the characteristics of the version relation between ontologies and at the identification of online ontologies. Then, it describes the design of a web-based system that helps users to manage changes in ontologies. The system helps to keep different versions of web-based ontologies interoperable, by maintaining not only the transformations between ontologies, but also the conceptual relation between concepts in different versions. The system allows ontology engineers to compare versions of ontology and to specify these conceptual relations. For the visualization of differences, it uses an adaptable rule-based mechanism that finds and classifies changes in RDF-based ontologies.