Principles for term obsoletion: Difference between revisions
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comment: This term was made obsolete because [reason]. | comment: This term was made obsolete because [reason]. | ||
==Alternatives for Obsolete Terms | |||
==Alternatives for Obsolete Terms== | |||
To suggest alternative terms, use the replaced_by and consider tags (described in the OBO format documentation). | To suggest alternative terms, use the replaced_by and consider tags (described in the OBO format documentation). | ||
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comment: Note that this term was reinstated from obsolete. | comment: Note that this term was reinstated from obsolete. | ||
[[Category: Curator_Guides]][[Category: Ontology]] | [[Category: Curator_Guides]][[Category: Ontology]] |
Revision as of 20:00, 25 May 2009
What is obsolete?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
Terms used for manual annotation, generic GO slim, or mappings
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.
An email is sent to the list with a structured subject line:
Alert: Proposal to obsolete GO:nnnnnnn: term that impacts existing annotation
The email should have this structure:
The proposal has been made to obsolete GO:nnnnnnn: term name. There exist today annotations to this term as follows (data from AmiGO): SGD: n objects FB: n objects MGD: n objects (etc., for all gene association data presented by AmiGO) *The term is used in the following mappings: db2go: external term ; ID -> GO:nnnnnnn: term *The term is found in the generic GO slim set. The reasons for this proposal are a brief summary of the technical case for change. The SourceForge discussion can be found at SourceForge url. UNLESS OBJECTIONS ARE RECEIVED BY date WE WILL ASSUME THAT YOU AGREE TO THIS CHANGE.
- Delete as appropriate.
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.
Changes will only be implemented if the following criteria are met:
- No objections are received from consortium members who have existing annotations to this term (i.e. those listed in the above e-mail).
- There is no one else who replies negatively to the proposal within 14 days.
- 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.
Both those with affected annotations and those without should preserve the subject line in their reply.
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.
Obsoletion of terms in the generic GO slim
If a term in the generic GO slim is obsoleted after agreement by the consortium we alert the GO friends mailing list.
Terms not used for manual annotation, generic GO slim, or mappings
Proposed obsoletion should be implemented two weeks after they are announced on SourceForge unless objections are raised.
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].
Alternatives for Obsolete Terms
To suggest alternative terms, use the replaced_by and consider tags (described in the OBO format 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:
comment: Note that this term was reinstated from obsolete.