Modification Annotation

Modifications are annotated in Canto on the gene product which is being modified (i.e the modified target).

Annotation extensions and qualifiers can be used to capture additional supporting data described below

Capturing Information about the modifier, or temporal features of the modification

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)	GO IDs are ​phases which are stored in the BP ontology
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	present_during(GO:0000080)	-
-	level_fluctuates_during	example required	-
-	occupancy	example required	-
-	required_for	example required	-

Capturing information about the modified residue(s)

Syntax for capturing the modified residue(s)

• 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, (NOTE THIS PAGE SAYS UNMODIFIED EXCEPT HISTONES describing residues modified or mutated
• 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.

Detiled syntax for compound vs. independent annotations =

• See AnnEx Syntax

• 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