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| [[Guide to obsoletion -v2 2018-08-06]]
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| ==What is obsolete?==
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| 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.
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| 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.
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| 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.
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| 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.
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| ==Term Obsoletion Protocol== | | ==Term Obsoletion Protocol== |
| | [[Obsoleting_an_Existing_Ontology_Term]] |
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| | ==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. |
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| The following [[Obsoleting_an_Existing_Ontology_Term]] 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 |
| | | ** 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].
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| E.g.
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| comment: This term was made obsolete because it represents a gene product.
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| comment: This term was made obsolete because it refers to a class of proteins.
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| comment: This term was made obsolete because it was added in error; it does not refer to a normal subcellular structure.
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| comment: This term was made obsolete because more specific terms were created.
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| comment: This term was made obsolete because it was an unnecessary grouping term.
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| comment: This term was made obsolete because the meaning of the term is ambiguous.
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| ==Alternatives for Obsolete Terms==
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| To suggest alternative terms, use the replaced_by and consider tags.
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| ===Exact replacement(s)===
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| 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:
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| example:
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| [Term]
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| id: GO:0005563
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| name: transfer RNA
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| namespace: molecular_function
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| def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah]
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| comment: This term was made obsolete because it represents a gene product.
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| is_obsolete: true
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| replaced_by: GO:0030533
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| ===No exact replacement(s)===
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| In cases where all existing annotations and mappings can't necessarily be transferred to one term, use the '''consider''' tag:
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| example:
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| [Term]
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| id: GO:0030464
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| name: ginger dependent sterility (sensu Fungi)
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| namespace: biological_process
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| def: "OBSOLETE (was not defined before being made obsolete)." [GOC:sgd_curators]
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| comment: This term was made obsolete because it reflected a trait or phenotype.
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| is_obsolete: true
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| consider: GO:0030466
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| ===Using multiple tags===
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| 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:
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| ====More than one replaced_by tag====
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| [Term]
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| id: GO:0016733
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| name: iron-iron nitrogenase activity
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| namespace: molecular_function
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| def: "OBSOLETE. Catalysis of the reaction: iron + iron = nitrogenase." [EC:1.18.6.1]
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| comment: This term was made obsolete because it represents a cellular component.
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| is_obsolete: true
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| replaced_by: GO:0016163
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| replaced_by: GO:0016611
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| ====More than one consider tag====
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| (also shows use of terms from two ontologies)
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| [Term]
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| id: GO:0016910
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| name: SAP kinase 3 activity
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| namespace: molecular_function
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| def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah]
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| comment: This term was made obsolete because it describes a gene product.
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| synonym: "SAPK3" EXACT []
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| is_obsolete: true
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| consider: GO:0004674
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| consider: GO:0004871
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| consider: GO:0007254
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| ====Consider and replaced_by tags both used====
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| [Term]
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| id: GO:0004207 | |
| name: effector caspase activity
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| namespace: molecular_function
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| def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah]
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| comment: This term was made obsolete because it includes biological process information.
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| is_obsolete: true
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| replaced_by: GO:0004197
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| consider: GO:0006915
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| 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.
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| 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.
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| ==Restoring obsolete terms==
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| If you need to reinstate an obsolete term back into the ontologies, use the following:
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| comment: Note that this term was reinstated from obsolete.
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| [[Category:Ontology]][[Category:GO Editors]][[Category:Editor_Guide_2018]] | | [[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]][[Category:To be reviewed]] |