Version 64 (modified by 6 years ago) (diff) | ,
---|
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