wiki:Modification

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

Modification Annotation

RNA mods, temp done as: controlled curation, RNA modification, blah details; dbxref=PMID:xxx.

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

Usage Relation Syntax (Example) Notes
data shows the identity of the modifieradded_by added_by(wee1)*ensure that you have annotated the modifier with the molecular fiunction and substrate
data shows identity of modification removerremoved_by removed_by(cdc25)ensure that you have annotated the modifier with the molecular fiunction and substrate
data shows "active" addition at a certain timeadded_during removed_during(GO:0000080)GO IDs are phases or processes
data shows "active" addition at a certain timeremoved_during removed_during(GO:0000080) GO IDs are phases or processes
data shows a modification is present, but not when it was addedpresent_during present_during(GO:0000080)GO IDs are phases or processes
data shows a modification is present, but not when it was addedabsent_during absent_during(GO:0000080)GO IDs are phases or processes
data shows a modification is present in a certain genomic locationcoincident_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 moleculehas_direct_inputhas_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 duringabsent_duringabsent_during(GO:0000080)GO IDs are phases or processes
data shows a modification is present in the presence of a chemicalin_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.

Syntax for structuring compound vs. independent annotations

Last modified 5 years ago Last modified on Oct 28, 2015, 12:37:50 PM