wiki:Modification

Version 3 (modified by vw253, 6 years ago) (diff)

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Modification (and other "substrate is" annotations)

Modification annotations are annotated on the gene product which is being modified (i.e the modified target)

Annotation extensions can be used to capture additional supporting data including

relation object example notes
added_by ID of modifier added_by(cwee1) ensure that you have annotated the modifier with the molecular fiunction and substrate
removed_by ID of modifier removed_by(cdc25) ensure that you have annotated the modifier with the molecular fiunction and substrate
added_during GO identifier exmaple required -
present_during GO identifier example required -
removed_during GO identifier example required -
absent_during GO identifier example required -
level_fluctuates_during GO identifier example required -
occupancy GO identifier example required -
required_for GO identifier example required -

(and if known, add the modified residues).

  • If you are adding the residues, and the residues numbers apply to a mature form of the protein, not the precursor translation, make sure that you request a pro ID for the shorter form, and put this in an annotation_extension has_direct_input(PR:xxxxx) so that the residues you specify matches the molecule in this extension.

  • If you know when the modification is (or isn't) present:
    • If the data shows "active" addition or removal at a certain time, use added_during or removed_during, e.g. annotation_extension=removed_during(GO:0000080)
    • Otherwise, you can use present_during or absent_during to make a less strong statement, e.g. annotation_extension=present_during(GO:0000080)
  • For annotations which involve a "target gene" of this type which are not "protein modification" annotations we only capture the target gene as an annotation extension, and the reciprocal annotation (gene B is TARGET_OF Gene A) will be inferred later