Select a resource, then modify its URI or name in the Name/URI text box of the Resource Editor's Form. Press Enter. Alternatively, right-click on a class, property or instance and select Rename...
If the ontology you are making changes to is imported by other ontologies in your workspace, TopBraid Composer will identify all the importing ontologies and then display a 'Select files to refactor' dialog asking if you want it to rename the resource for all models. We advise that you let Composer to apply the rename to all the files in order to maintain consistency. If you do not want it to perform the rename everywhere, uncheck the select boxes of the models to which rename should not be applied. Note that you can review the changes before they are saved.