Changes between Initial Version and Version 1 of Modification


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Timestamp:
Jan 27, 2015, 1:23:52 PM (6 years ago)
Author:
vw253
Comment:

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  • Modification

    v1 v1  
     1== Modification (and other "substrate is" annotations) ==
     2 
     3 * Make the modification annotation explicitly on the molecule which is being modified (and if known, add the modified residues).
     4  * 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.
     5  * See [wiki:AnnotationExtensionSyntax AnnEx Syntax] and [wiki:DescribingResidues describing residues modified or mutated] for "residue=" syntax
     6 * If you have information which kinase/phosphatase etc alters which residue
     7  * use the added_by or removed_by relationship in an annotation extension on the modification
     8  * 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.
     9 * If you know when the modification is (or isn't) present:
     10  * 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)
     11  * Otherwise, you can use present_during or absent_during to make a less strong statement, e.g. annotation_extension=present_during(GO:0000080)
     12 * 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
     13