Changes between Version 65 and Version 66 of GOAnnotationGuidelines


Ignore:
Timestamp:
Feb 25, 2015, 5:39:24 PM (6 years ago)
Author:
vw253
Comment:

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  • GOAnnotationGuidelines

    v65 v66  
    6262   *  When to make a GO process  annotation 
    6363      *   GO or phenotype
    64      
    65 
    66     * Regulation
     64 
     65   * Regulation
    6766       *  [http://www.geneontology.org/GO.annotation.conventions.shtml#regulationTerms  GOC Regulation]
    6867       *  Lots of ongoing discussion among !PomBase curators and with other GO annotators, about when to annotate to regulation terms and when not.
     
    7069       
    7170    * Transcription
    72     * [http://wiki.geneontology.org/index.php/Transcription Transcription Overhaul details]
    73     * For  "Transcription factors" see Molecular Function below
    74    * Annotate to regulation of transcription (with extensions as appropriate) only if there isn't enough data to support annotating to a transcription factor MF term (descendant of GO:0003700 sequence-specific DNA binding transcription factor activity); if there is a transcription factor MF annotation, a transcription regulation BP annotation will be inferred by transitivity
    75   * All fission yeast annotations for RNAi so far should be to the term [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0031048 chromatin silencing by small RNA (GO:0031048)]
    76    * Note that the GO term [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0016246 RNA interference (RNAi; GO:0016246)] is not an ancestor of GO:0031048, because in GO RNAi is defined more strictly, according to the original "post-transcriptional" usage.
    77 
    78  * Regulation of transcription and signalling pathways
    79 Regulation of transcription and signalling pathways Consists of four components: a signal transduction cascade, a transcription factor, the process of transcription and a downstream process. The signal transduction cascade regulates the downstream process ONLY. The transcription factor regulates transcription AND the downstream process. For instance, the transcription factor ste11 should be annotated to positive regulation of transcription involved in sporulation AND signal transduction involved in positive regulation of sporulation. Mam2 in contrast is only annotated to signal transduction involved in positive regulation of sporulation.
     71       * [http://wiki.geneontology.org/index.php/Transcription Transcription Overhaul details]
     72       * For  "Transcription factors" see Molecular Function below
     73       * Annotate to regulation of transcription (with approtiate gene specific extensions) only if there isn't enough data to support annotating to a transcription factor MF term
     74 
     75    * Regulation of transcription and signalling pathways
     76       * Regulation of transcription and signalling pathways Consists of four components:  A signal transduction cascade, a transcription factor, the process of transcription and a downstream process. The signal transduction cascade regulates the downstream process ONLY. The transcription factor regulates transcription AND the downstream process.  For example:
     77            * Transcription factor ste11 should be annotated to positive regulation of transcription involved in sporulation AND signal transduction involved in positive regulation of sporulation.
     78            * Mam2 in contrast is only annotated to signal transduction involved in positive regulation of sporulation.
    8079
    8180 * Transport/Localization