wiki:Modification

Version 2 (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

  • The molecule doing the modifying (i.e the protein kinase for a phosphorylation, the phosphatase for dephosphorylation)
    • In this case you should ensure that you have annotated the modifier with the molecular fiunction and substrate

(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.
  • See AnnEx Syntax and describing residues modified or mutated for "residue=" syntax
  • If you have information which kinase/phosphatase etc alters which residue
    • use the added_by or removed_by relationship in an annotation extension on the modification
    • Also, add the target as an annotation_extension=has_substrate(PomBase:substrate_gene_ID) to the function activity (or process if there is no function). Later we will be able add reciprocal annotations automatically.
  • If you know when the modification is (or isn't) present:
    • If the data shows "active" addition or removal at a certain time, use added_during or removed_during, e.g. annotation_extension=removed_during(GO:0000080)
    • 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