We investigate the problem of automatically repairing inconsistent ontologies. A repair is triggered when a contradiction is detected between the current theory and new experimental evidence. We are working in the domain of physics because it has good historical records of such contradictions and how they were resolved. We use these records to both develop and evaluate our techniques. To deal with problems of inferential search control and ambiguity in the atomic repair operations, we have developed ontology repair plans, which represent common patterns of repair. They first diagnose the inconsistency and then direct the resulting repair. Two such plans have been developed to repair ontologies that disagree over the value and the dependence of a function, respectively. We have implemented the repair plans in the galileo system and successfully evaluated galileo on a diverse range of examples from the history of physics.