Changes between Version 154 and Version 155 of MatrixProject


Ignore:
Timestamp:
Jan 3, 2013, 12:03:52 PM (9 years ago)
Author:
val_wood
Comment:

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  • MatrixProject

    v154 v155  
    1313 * Identify annotation errors (curated and automated)
    1414   * Allows rapid detection of incorrect mappings
    15    * Allows detection of "Indirect downstream 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)
     15   * Allows detection of "Indirect downstream 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 embryonic 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)
    1616     * Examples:
    1717     * splicing -> cell cycle)
     
    5353|| term ID 1 || term ID 2|| term name 2|| exceptions (everything in this column which is NOT a GO ID or "OR/AND" needs to be in brackets|| comments/checked in species ||
    5454||GO:0006520 || GO:0006310 || DNA recombination || NO OVERLAP || S.p; M.m; S.c. ||
    55 ||GO:0006520 || GO:0006281 || DNA repair || GO:0006521 (regulation of cellular amino acid metabolic process -NOTE transcriptional) OR GO:0006338 (chromatin remodelling- NOTE, this may be indirect for repair???) ||S.p; M.m (one bad IP mapping reported); S.c. (one query)||
     55||GO:0006520 || GO:0006281 || DNA repair || GO:0006521 (regulation of cellular amino acid metabolic process -NOTE transcriptional) OR GO:0006338 (chromatin remodelling- NOTE, this may be indirect for repair???) ||S.p; M.m (one bad IP mapping reported); S.c.||
    5656||GO:0006520 || GO:0006260 || DNA replication || NO OVERLAP ||S.p; M. m (one bad IP mapping reported); S.c (3 queried) ||
    5757||GO:0006520 || GO:0030437 || ascospore formation || NO OVERLAP ||S.p; M.m (n/a); S.c. ||
     
    115115||SGD || FPR1 || replaced arginine metabolic process with "regulation of arginine metabolic process ||upstream regulation||
    116116||SGD || CBF1 || methionine biosynthetic process ||downstream/indirect||
    117 
     117|| MGI|| Sod1 || query nucleotide excision repair IMP || incorrect interpretation||
    118118
    119119