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).
This situation can arise in a number of different ways:
For more on obsoletion workflows, see the obsoletion guide 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). 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
robot repair \ --input xref-need-of-repair.obo \ --annotation-property oboInOwl:hasDbXref \ --output results/xref-repaired.obo