Principles for term obsoletion
(Redirected from Curator Guide: Obsoletion)
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 using an annotation
owl:deprecated:true, 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 GO term is associated with its definition rather than with the term name. If the wording of a definition is changed without changing its meaning, the GO term stays. A new meaning requires a new GO ID, even if the term name doesn't change.
Cases in which a term may be obsoleted
- Changes in term definition that invalidates existing annotations or other usage of the ontology
- Major 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
- Newer finding that invalidate the biology that the term represents, for example, artifactual cellular components; enzymatic reactions for which no enzyme has been identified
- More examples are listed here: Obsoleting_an_Existing_Ontology_Term#Possible_reasons_for_obsoletion
Cases in which a term should not be obsoleted
- 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 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.
- GO ontology editors should be conservative when obsoleting terms, as this causes large potential impact on annotations, on other ontologies using GO, and on the stability of analysis results using GO. Obsoletions should be done only when a change in definition would make existing GO usages incorrect and correction is needed.
A trivial example that illustrates when a should not or should be obsoleted
Assume that there is a term mouse, GO ID GO:0000123, in an ontology; it is defined as A small furry mammal. If the term name is changed to Mus musculus and the definition remains the same, the GO ID stays the same because the meaning stays the same. On the other hand, if the definition changes to A piece of computer equipment, then the old term should be made obsolete category, and mouse as newly defined, gets a new GO ID, GO:0000456.
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.