Obsoleting and replacing entities

The odk:obsolete-replace command is intended to obsolete an entity and replace all its usages with a replacement entity in a single operation.

This is useful when merging terms or when an entity needs to be retired but its usages should be redirected to another term.

Basic usage

The command requires two options:

--obsolete <TERM>: The entity to obsolete (CURIE or IRI)
--replacement <TERM>: The replacement entity (CURIE or IRI)

Example:

robot odk:obsolete-replace --input ontology.owl \
                           --obsolete EXAMPLE:0000001 \
                           --replacement EXAMPLE:0000002 \
                           --output output.owl

What the command does

When executed, the command performs the following operations:

Replaces all usages of the obsolete entity with the replacement entity throughout the ontology (in all axioms)
Removes annotations from the obsolete entity: label, comment, and definition (IAO:0000115)
Marks the obsolete entity as deprecated by adding an owl:deprecated true annotation
Adds a new label to the obsolete entity, prefixed with “obsolete” (e.g., “obsolete old term name”)
Adds the original label as an exact synonym on the replacement entity, with a database cross-reference annotation pointing to the obsolete entity
Adds a “term replaced by” annotation (IAO:0100001) on the obsolete entity pointing to the replacement entity

Example workflow

A typical workflow might look like:

robot merge --input ontology.owl \
      odk:obsolete-replace --obsolete GO:0000001 \
                           --replacement GO:0000002 \
      annotate --ontology-iri http://example.org/ontology.owl \
               --output output.owl

This merges the ontology, obsoletes GO:0000001 replacing it with GO:0000002, and then annotates and saves the result.