Changes between Version 108 and Version 109 of MatrixProject


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Timestamp:
Nov 7, 2012, 11:18:12 AM (9 years ago)
Author:
val_wood
Comment:

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  • MatrixProject

    v108 v109  
    1212Querying annotation overlaps is a powerful method to:
    1313 * Identify annotation errors (curated and automated)
    14    * allows rapid detection of incorrect mappings
     14   * Allows rapid detection of incorrect mappings
     15   * Allows detection of "Indirect upstream effects". One process acts upstream of another and if the upstream process is "broken" there is an indirect downstream effect, these are usually annotated from mutant phenotypes. Would the term x involved in y make sense (for example splicing involved in embroyonic development)? if not, probably the effect is indirect (I'm not sure if this is a good criteria to distinguish but it sounds as though it could be?). (Note: PomBase and SGD already do not annotate these as biological processes, they are captured with "phenotype" annotations)
     16     * Examples:
     17     * splicing -> cell cycle)
     18     * add more examples
    1519 * Experimental errors (mainly from legacy data where newer papers have changed viewpoint)
    1620 * Identify problems in the gene ontology
     
    2327
    2428 *  Annotation to a term which is a child of both terms i.e pentose phosphate shunt is a child of nucleotide metabolism and carbohydrate metabolism. tRNA acetylation is a child or tRNA metabolism and amino acid metabolism
    25 
    26  * Indirect upstream effects
    27    * One process acts upstream of another and if the upstream process is "broken" there is an indirect downstream effect, these are usually annotated from mutant phenotypes. Would the term x involved in y make sense (for example splicing involved in embroyonic development)? if not, probably the effect is indirect (I'm not sure if this is a good criteria to distinguish but it sounds as though it could be?)
    28      * Examples:
    29      * splicing -> cell cycle)
    30      * add more examples
    31 
    32 Note PomBase and SGD do not annotate these as bioloical processes, they are captures with "phenotype" annotations)
    3329
    3430