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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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| ===Terms used for manual annotation, generic GO slim, or mappings=== | | ==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. |
| When there is a proposal to obsolete a term that has been used by a consortium group for manual annotation, for mappings, or as part of the generic GO slim, the following standard operating procedure should be used to notify the group.
| | * Obsolete terms lose their relationships to other terms. |
| | | * Obsolete terms are identified in the OBO format flat file by the 'is_obsolete: true' tag. |
| An email is sent to the list with a structured subject line:
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| Alert: Proposal to obsolete GO:nnnnnnn: term that impacts existing annotation
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| The email should have this structure:
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| The proposal has been made to obsolete GO:nnnnnnn: term name.
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| There exist today annotations to this term as follows (data from AmiGO):
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| SGD: n objects
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| FB: n objects
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| MGD: n objects
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| (etc., for all gene association data presented by AmiGO)
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| *The term is used in the following mappings:
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| db2go: external term ; ID -> GO:nnnnnnn: term
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| *The term is found in the generic GO slim set.
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| The reasons for this proposal are a brief summary of the technical case for change.
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| The SourceForge discussion can be found at SourceForge url.
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| UNLESS OBJECTIONS ARE RECEIVED BY date WE WILL ASSUME THAT YOU AGREE TO THIS CHANGE.
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| *Delete as appropriate.
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| Note: the reason for using AmiGO here, and not all of the gene association files, is both for simplicity and because the major impact of these changes is on manually curated, rather than computationally predicted, annotations.
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| Changes will only be implemented if the following criteria are met:
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| *No objections are received from consortium members who have existing annotations to this term (i.e. those listed in the above e-mail).
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| *There is no one else who replies negatively to the proposal within 14 days.
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| *If there is any consortium member who very strongly opposes this change, and agreement is not reached by email, then the proposal will be put on the agenda for discussion at the next Consortium meeting.
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| Both those with affected annotations and those without should preserve the subject line in their reply.
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| We hope, of course, that consensus can be reached without the need for a face-to-face discussion at our next meeting. However, the consequences of some of these changes for the annotating groups are quite severe in terms of the work needed to reannotate, and we consider that it is most reasonable for such changes to be made only after all have had a chance to discuss both the case for change and its implications.
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| ===Obsoletion of terms in the generic GO slim===
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| If a term in the generic GO slim is obsoleted after agreement by the consortium we alert the GO friends mailing list.
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| ===Terms not used for manual annotation, generic GO slim, or mappings===
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| Proposed obsoletion should be implemented two weeks after they are announced on SourceForge unless objections are raised.
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| ==Comments for Obsolete Terms==
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| 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.
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| Use the following syntax for the reason for obsoletion:
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| comment: This term was made obsolete because [reason].
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| ==Alternatives for Obsolete Terms===
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| To suggest alternative terms, use the replaced_by and consider tags (described in the OBO format documentation).
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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: 8 reduced ferredoxin + 8 H+ + N2 + 16 ATP = 8 oxidized ferredoxin + 2 NH3 + 16 ADP + 16 phosphate." [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
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| 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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| ==Term Merges, Splits and Movements==
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| ===Term merges===
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| Terms are merged in cases where two terms have exactly the same meaning. Usually this situation arises when one term exists, and another wording of the same concept is added as a new term instead of as a synonym, either because a curator didn't find the old term or didn't know it meant the same thing.
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| When two terms are merged, e.g. term A and term B are merged into term A, the GO ID of term B is made a secondary GO ID, and the term string is made a synonym. Usually, the ID that has existed longer is used as the primary ID, but exceptions can be made; for example, the term string of the newer ID may be more correct or the definition may be better.
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| Secondary GO IDs are stored in the OBO flat file with the 'alt_id' tag.
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| ===Term splits=== | | ==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. |
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| A term can be split if curators decide that it combines two or more concepts that should be represented by separate terms.
| | ==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. |
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| The standard procedure for splitting a term is to obsolete the original term and add a comment directing annotators to the new term.
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| ===Moving terms===
| | [[Ontology_Development#Editing_the_Ontology |Back to: Editing the Ontology]] |
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| Terms can be moved as long as the term's new position does not break the true path rule. Terms should not, however, be moved between ontologies; only within the same ontology. If you need to move a term to a different ontology, first obsolete it and then create a new term in the other ontology.
| | [[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]][[Category:To be reviewed]] |