Changes between Version 2 and Version 3 of Modification


Ignore:
Timestamp:
Jan 27, 2015, 1:37:43 PM (6 years ago)
Author:
vw253
Comment:

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  • Modification

    v2 v3  
    55 Annotation extensions can be used to capture additional supporting data including
    66
    7    * The molecule doing the modifying (i.e the protein kinase for a phosphorylation, the phosphatase for dephosphorylation)
    8       * In this case you should ensure that you have annotated the  modifier with the molecular fiunction and substrate
    9  
     7   
     8|| relation || object || example || notes||
     9|| added_by || ID of modifier || added_by(cwee1) || ensure that you have annotated the  modifier with the molecular fiunction and substrate||
     10|| removed_by || ID of modifier || removed_by(cdc25)|| ensure that you have annotated the  modifier with the molecular fiunction and substrate||
     11||added_during|| GO identifier || exmaple required|| -||
     12|| present_during|| GO identifier || example required|| -||
     13||removed_during || GO identifier || example required|| -||
     14|| absent_during || GO identifier || example required|| -||
     15||level_fluctuates_during || GO identifier || example required|| -||
     16||occupancy || GO identifier || example required|| -||
     17||required_for || GO identifier || example required|| -||
     18
    1019
    1120(and if known, add the modified residues).
    1221  * 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.
    13   * See [wiki:AnnotationExtensionSyntax AnnEx Syntax] and [wiki:DescribingResidues describing residues modified or mutated] for "residue=" syntax
    14  * If you have information which kinase/phosphatase etc alters which residue
    15   * use the added_by or removed_by relationship in an annotation extension on the modification
    16   * 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.
     22 
     23 * See [wiki:AnnotationExtensionSyntax AnnEx Syntax] and [wiki:DescribingResidues describing residues modified or mutated] for "residue=" syntax
     24
     25
    1726 * If you know when the modification is (or isn't) present:
    1827  * 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)