Principles for term obsoletion

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Term Obsoletion Protocol

Obsoleting an Existing Ontology Term

What is an obsolete GO term?

  • Terms removed from the ontology are not deleted, but tagged obsolete, so that any GO ID ever created remains in the ontology.
  • Obsolete terms lose their relationships to other terms.
  • Obsolete terms are identified in the OBO format flat file by the 'is_obsolete: true' tag.

When is a term made obsolete?

  • A term can become obsolete when:
    • it is redefined in a way that invalidates existing annotations or other usage of the ontology
    • ontology term creation guidelines change (for example, the development of GO-CAM models may result in a GO term being obsoleted in favor of producing annotations using GO-CAM that represent the same concept)
    • the biology that the term represents is found to be flawed (for example artifactual cellular components)
    • specific examples are listed here: Obsoleting_an_Existing_Ontology_Term#Possible_reasons_for_obsoletion
  • Changes in term label or definition that do not alter the meaning of the term do not usually lead to obsoletion. On the other hand, when a term's definition changes meaning, the term should be obsoleted and a new term created instead. In this case, ontology editors usually add a tag 'consider: new term ID', or 'replaced by: new term ID'.
  • The fact that a term is has incorrect annotations associated does not usually lead to term obsoletion; ideally the database that submitted the annotations should be informed of the error instead.

Restoring an obsolete GO term

In rare cases, obsolete GO terms may be restored, if the original meaning is conserved. In this case, an ID that had been obsolete at some point becomes a valid ID.

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