Adding more details to repair
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](http://purl.obolibrary.org/obo/IAO_0100001)).
+This situation can arise in a number of different ways:
+
+ 1. When you are editing an ontology in Protege, you obsolete a class, but forget to repair axioms that reference this.
+ 2. When you rebuild an import module using [extract](extract), and the upstream ontology has obsoleted classes that you are using.
+
+For more on obsoletion workflows, see the [obsoletion guide](https://ontology-development-kit.readthedocs.io/en/latest/ObsoleteTerm.html) in the Ontology Development Kit documentation.
+
+To repair an ontology (with the name `need-of-repair.owl`) run the following command:
+
robot repair \
--input need-of-repair.owl \
--output results/repaired.owl
+This will generate a new file `results/repaired.owl`. You can compare this with the original file (either using unix `diff` or [robot diff](diff)). If the changes that were made look good then you can simply replace the source file with the repaired file (`mv results/repaired.owl need-of-repair.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 `--annotation-properties-file`:
