Principles for term obsoletion: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
(13 intermediate revisions by 3 users not shown)
Line 1: Line 1:
==What is obsolete?==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==
==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.


The following [http://wiki.geneontology.org/index.php/Editor_Guide#GO_Term_Obsoletion_Mails procedure]] should be used by ontology editors when emailing the GO lists regarding obsoletion notifications.
==When is a term made obsolete?==
 
* A term can become obsolete when:  
==Comments for Obsolete Terms==
** 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)
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.
** 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]]
Use the following syntax for the reason 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.
comment: This term was made obsolete because [reason].
 
 
==Alternatives for Obsolete Terms==
 
To suggest alternative terms, use the replaced_by and consider tags (described in the OBO format [http://www.geneontology.org/GO.format.obo-1_2.shtml documentation]).
 
===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:
==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.


comment: Note that this term was reinstated from obsolete.


[[Ontology_Development#Editing_the_Ontology |Back to: Editing the Ontology]]


[[Category: Curator_Guides]][[Category: Ontology]]
[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]][[Category:To be reviewed]]

Revision as of 12:36, 24 August 2020

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.


Back to: Editing the Ontology

Retrieved from "https://wiki.geneontology.org/index.php?title=Principles_for_term_obsoletion&oldid=78624"