wiki:Modification

Version 50 (modified by vw253, 7 years ago) (diff)

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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 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
  • 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
  • the residues numbers apply to the precursor translation, except for histones which are numbered assuming removal of the initiator methionine
  • By default residues reported will refer to the full length 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