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 or processes
data shows "active" addition at a certain time	removed_during	removed_during(GO:0000080)	GO IDs are ​phases or processes
data shows a modification is present, but not when it was added	present_during	present_during(GO:0000080)	GO IDs are ​phases or processes
data shows a modification is present, but not when it was added	absent_during	absent_during(GO:0000080)	GO IDs are ​phases or processes
data shows a modification is present in a certain genomic location	coincident_with	coincident_with(SO: subtelomeric region)	SO ID for genomic location, usually used with histones. DEPRACATED, this will be removed after V48. Instead request a PRO ID for the modification and use column 17 with component
modification refers to residue numbering in a processed molecule	has_direct_input	has_direct_input(PRO:ID)	e.g. Leucine removal of mating pheromone map2 refers to leu23 in processed molecule, OR if the input is the PRO ID of a previously modified molecule
modification not present during	absent_during	absent_during(GO:0000080)	GO IDs are ​phases or processes
data shows a modification is present in the presence of a chemical	in_presence_of(	in_presence_of(GO:0000080)	CHEBI ID

• this information will be used to add a reciprocal "Target_of" annotation to the wee1 gene page

Capturing information about the modified residue(s)

Syntax for capturing the modified residue(s)

• residue=S204
• residue=S204,S205,T206

• By default residues reported will refer to the full length precursor translation. if the residues numbers you report refer to a modified (shortened) form (as in the case of histones) of the 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 describing residues modified or mutated for "residue=" syntax for more details of the residue describing syntax

Syntax for structuring compound vs. independent annotations

• See AnnEx Syntax