Version 11 (modified by 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
usage | relation | example | notes |
data shows the identity of the modifier | added_by | added_by(wee1) | ensure that you have annotated the modifier with the molecular fiunction and substrate |
data shows identity of modification remover | removed_by | removed_by(cdc25) | ensure that you have annotated the modifier with the molecular fiunction and substrate |
data shows "active" addition at a certain time | added_during | removed_during(GO:0000080) | - |
data shows "active" addition at a certain time | removed_during | removed_during(GO:0000080) | - |
data shows a modification is present but not when it was added | present_during | present_during(GO:0000080) | - |
data shows a modification is present but not when it was added | absent_during | example required | - |
- | level_fluctuates_during | example required | - |
- | occupancy | example required | - |
- | required_for | 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.
- See AnnEx Syntax and describing residues modified or mutated for "residue=" syntax
- If you know when the modification is (or isn't) present:
- 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