ROBOT rename command
The rename command provided by the SSSOM plugin does a similar thing as the standard rename command in ROBOT: it renames entities in the source ontology. The difference with the standard command is that it uses a SSSOM mapping set as source of truth for which entity should be renamed into what, instead of the ad-hoc, dual-column TSV format used by the standard command.
1. Usage
The command just needs the --sssom option, which indicates the file containing the mapping set to use for renaming. Any entity within the ontology that has an IRI that is the subject of one of the mappings will be renamed to the IRI of the object of that same mapping.
The --sssom option may be repeated as many times as needed to read mappings from more than one file. All mapping sets will be combined before the renaming operation is performed.
2. Selecting mappings to use
By default, only mappings whose mapping predicate is http://purl.obolibrary.org/obo/IAO_0100001 (“term replaced by”) will be considered.
To explicitly specify another mapping predicate, use the --predicate option. That option may be repeated as many times as desired to select mappings based on several predicates.
To use all mappings regardless of their mapping predicate, use the special value all (or any) to the --predicate option.
3. Updating labels
If the --labels option is used, and the mapping set contains object_label metadata, then in addition to changing the IRI the command will also update the label of the class or property that is being renamed, using the object_label slot of the mapping as the new label.