Version 20 (modified by 6 years ago) (diff) | ,
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Modification Annotation
Modifications are annotated in Canto 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 | Syntax (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 | - |
Capturing the modified residue(s)
Syntax Examples
residue=S204 residue=S204|S205|T206 *Question IS THIS CORRECT???
- the residues numbers apply to the 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 for the full syntax for compound and independent annotations
- See describing residues modified or mutated for "residue=" syntax (NOTE I THINK WE SHOULD REMOVE THE STUFF ABOUT MODIFICATION RESIDUE SYNTAX FROM THIS PAGE)
I DON"T UNDERSTSTAND THIS COMMENT 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