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