Modification (and other "substrate is" annotations)

• Make the modification annotation explicitly on the molecule which is being modified (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