Principles for merging terms: Difference between revisions

Revision as of 12:49, 26 October 2020

Merge Procedure

What is a GO term merge?

Term merges result from two or more terms being subsumed into a single term.

When are GO terms merged?

Common reasons to merge terms include:

Terms have exactly the same meaning
The meaning is too close to support consistent, distinct annotations
The distinction between a parent and a child is not useful or necessary in the scope of GO

Care should be taken when merging terms that may be used elsewhere, because it may create false assertions (annotations), in particular NOT. Also if terms are used for logical definitions, then that may create incorrect assertions.

TO PROPOSE AT AN ANNOTATION CALL: Whenever possible, obsolete term with 'REPLACED BY' rather than merging terms.

What happens when GO terms are merged?

When terms are merged, e.g. term A and term B are merged into term A, the GO ID of term B is made an alternative (secondary) GO ID, and the term string is made a synonym. Secondary GO IDs remain in GO with the 'alt_id' tag.

  ++ Add example

Review Status

Last reviewed:

Back to: Editing the Ontology

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-Term Merges, Splits and Movements
+==Merge Procedure==
+[[Merging Ontology Terms]]
-[[Merge Split Move v2 2018-08-06]]
+==What is a GO term merge?==
+Term merges result from two or more terms being subsumed into a single term.
-==Term merges==
+==When are GO terms merged?==
+Common reasons to merge terms include:
+* Terms have exactly the same meaning
+* The meaning is too close to support consistent, distinct annotations
+* The distinction between a parent and a child is not useful or necessary in the scope of GO
-Terms are merged in cases where two terms have exactly the same meaning or when the meaning is too close to support consistent, distinct annotations. 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.
-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 an alternative (secondary) GO ID, and the term string is made a synonym (see documentation on synonym types). 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.
+Care should be taken when merging terms that may be used elsewhere, because it may create false assertions (annotations), in particular NOT. Also if terms are used for logical definitions, then that may create incorrect assertions.
-Secondary GO IDs are stored in the OBO flat file with the 'alt_id' tag.
+TO PROPOSE AT AN ANNOTATION CALL: '''Whenever possible, obsolete term with 'REPLACED BY' rather than merging terms'''.
-==Term splits==
+==What happens when GO terms are merged?==
+When terms are merged, e.g. term A and term B are merged into term A, the GO ID of term B is made an alternative (secondary) GO ID, and the term string is made a synonym. Secondary GO IDs remain in GO with the 'alt_id' tag.
-A term can be split if curators decide that it combines two or more concepts that should be represented by separate terms.
+   ++ Add example
-The standard procedure for splitting a term is to obsolete the original term and add to add 'consider' tags for the old term ID to all new terms. It's also good practice to add a comment explaining why the term was split, e.g.:
- id: GO:0004327
+== Review Status ==
- name: formaldehyde dehydrogenase (glutathione) activity
- namespace: molecular_function
- def: "OBSOLETE. Catalysis of the reaction: formaldehyde + glutathione + NAD+ = S-formylglutathione + NADH + H+." [EC:1.2.1.1]
- comment: This term was made obsolete because it was derived from an EC entry (1.2.1.1) that has since been split into two entries.
- subset: gosubset_prok
- xref: UM-BBD_enzymeID:e0028
- is_obsolete: true
- consider: GO:0051903
- consider: GO:0051907
-==Moving terms==
+Last reviewed:
-Terms can be moved as long as the term's new position correctly reflects its relationships to other terms and moving the term does not imply a significant change in the meaning of the term. 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.
+[[Ontology_Development#Editing_the_Ontology |Back to: Editing the Ontology]]
+[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]][[Category:To be reviewed]]
-[[Category:Curator_Guides]][[Category:Ontology]]