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 remain in the ontology.
  • Obsolete terms looses 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
    • 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.