Changes between Version 13 and Version 14 of Modification


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Timestamp:
Jan 27, 2015, 1:56:05 PM (6 years ago)
Author:
vw253
Comment:

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  • Modification

    v13 v14  
    11== Modification (and other "substrate is" annotations) ==
    22 
    3  Modification annotations are annotated on the gene product which is being modified  (i.e the modified target)
    4 
    5  Annotation extensions can be used to capture additional supporting data including
     3  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
    64
    75   
    8 ||Usage ||Relation || Example ||Notes||
     6||Usage ||Relation || Syntax (Example) ||Notes||
    97||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||
    108||data shows identity of modification remover||removed_by ||removed_by(cdc25)||ensure that you have annotated the  modifier with the molecular fiunction and substrate||
     
    1816
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    20 (and if known, add the modified residues).
    21   * 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.
     18 Capturing the modified residues
     19  Syntax  residue=S204
     20
     21  * the residues numbers apply to the mature form of the protein, not the precursor translation,
     22  * 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.
    2223 
    2324 * See [wiki:AnnotationExtensionSyntax AnnEx Syntax] and [wiki:DescribingResidues describing residues modified or mutated] for "residue=" syntax
    24  * If you know when the modification is (or isn't) present:
    25  
    26   * Otherwise, you can use present_during or absent_during to make a less strong statement, e.g. annotation_extension=present_during(GO:0000080)
     25
    2726 * 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
    2827