ROBOT can repair certain problems encountered in ontologies. So far, this is limited to updating axioms pointing to deprecated classes with their replacement class (indicated using term replaced by).
robot repair \ --input need-of-repair.owl \ --output results/repaired.owl
By default, annotation axioms are not migrated to replacement classes. However, this can be enabled for a list of annotation properties passed either as arguments to
--annotation-property or in a term file
robot repair \ --input xref-need-of-repair.obo \ --annotation-property oboInOwl:hasDbXref \ --output results/xref-repaired.obo