wiki:Modification

Version 10 (modified by vw253, 6 years ago) (diff)

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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 timeadded_during removed_during(GO:0000080)-
data shows "active" addition at a certain timeremoved_during removed_during(GO:0000080) -
data shows a modification is present but not when it was addedpresent_during present_during(GO:0000080)-
data shows a modification is present but not when it was added absent_during example required-
-level_fluctuates_during GO identifier example required -
-occupancy GO identifier example required-
-required_for GO identifier 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.

  • 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