Curator Guide: Obsoletion

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Guide to obsoletion -v2 2018-08-06

What is obsolete?

A term that is no longer used is not deleted, but is tagged obsolete. Never delete a GO ID: GO IDs should be conserved at all times so that, even if a term is defunct or has a new GO ID, someone searching using the old GO ID can find it.

A term can become obsolete when it is removed or redefined, but a term should not not be made obsolete due to changes in wording that do not alter the meaning of the term (see the documentation on redefining terms). When a term's definition changes meaning, the term should also be assigned a new GO ID, and the old ID considered obsolete.

As a general rule, if the annotations to a GO term would need to be changed as a result of the term definition changing, the term should be made obsolete. However, terms should not be made obsolete on the basis of incorrect annotations; the database that submitted the annotations should be informed of the error instead.

In the browser AmiGO and in OBO-Edit, an obsolete term becomes a child of the meta node obsolete. Obsolete terms are identified in the OBO format flat file by the 'is_obsolete: true' tag.


Term Obsoletion Protocol

The following Obsoleting_an_Existing_Ontology_Term should be used by ontology editors when emailing the GO lists regarding obsoletion notifications.

Comments for Obsolete Terms

When you make a term obsolete, insert the word 'OBSOLETE.' at the beginning of the term definition and add a comment that explains why the term has become obsolete and suggests alternative terms for annotators to use.

Use the following syntax for the reason for obsoletion:

comment: This term was made obsolete because [reason].
E.g.
comment: This term was made obsolete because it represents a gene product.
comment: This term was made obsolete because it refers to a class of proteins.
comment: This term was made obsolete because it was added in error; it does not refer to a normal subcellular structure.
comment: This term was made obsolete because more specific terms were created.
comment: This term was made obsolete because it was an unnecessary grouping term.
comment: This term was made obsolete because the meaning of the term is ambiguous.


Alternatives for Obsolete Terms

To suggest alternative terms, use the replaced_by and consider tags.

Exact replacement(s)

If exact replacement is possible (i.e. it is safe to move all existing annotations, keyword mappings, etc. to a suggested term), use the replaced_by tag:

example:

[Term] 
id: GO:0005563 
name: transfer RNA 
namespace: molecular_function 
def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] 
comment: This term was made obsolete because it represents a gene product. 
is_obsolete: true 
replaced_by: GO:0030533

No exact replacement(s)

In cases where all existing annotations and mappings can't necessarily be transferred to one term, use the consider tag:

example:

[Term] 
id: GO:0030464  
name: ginger dependent sterility (sensu Fungi) 
namespace: biological_process 
def: "OBSOLETE (was not defined before being made obsolete)." [GOC:sgd_curators] 
comment: This term was made obsolete because it reflected a trait or phenotype. 
is_obsolete: true 
consider: GO:0030466

Using multiple tags

It is possible to use more than one replaced_by or consider tags, or to combine them. Suggested terms may be chosen from more than one ontology. Examples:

More than one replaced_by tag

[Term]
id: GO:0016733 
name: iron-iron nitrogenase activity 
namespace: molecular_function 
def: "OBSOLETE. Catalysis of the reaction: iron + iron = nitrogenase." [EC:1.18.6.1] 
comment: This term was made obsolete because it represents a cellular component. 
is_obsolete: true 
replaced_by: GO:0016163 
replaced_by: GO:0016611

More than one consider tag

(also shows use of terms from two ontologies)

[Term] 
id: GO:0016910 
name: SAP kinase 3 activity 
namespace: molecular_function 
def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] 
comment: This term was made obsolete because it describes a gene product. 
synonym: "SAPK3" EXACT [] 
is_obsolete: true 
consider: GO:0004674 
consider: GO:0004871 
consider: GO:0007254

Consider and replaced_by tags both used

[Term] 
id: GO:0004207 
name: effector caspase activity 
namespace: molecular_function 
def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] 
comment: This term was made obsolete because it includes biological process information. 
is_obsolete: true 
replaced_by: GO:0004197 
consider: GO:0006915

Note: the consider and replaced_by tags are used in the OBO format version 1.2 files. In the OBO format 1.0 files, these tags are converted to text comments.

Note: to add consider or replaced_by tags in OBO-Edit, drag the suggested term, drop it onto an obsolete term, and choose 'set consider term' or 'set replacement term' from the popup menu; repeat as needed to add multiple terms.

Restoring obsolete terms

If you need to reinstate an obsolete term back into the ontologies, use the following:

comment: Note that this term was reinstated from obsolete.