Changes between Version 10 and Version 11 of GOAnnotationGuidelines


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Timestamp:
Mar 3, 2014, 1:51:34 PM (7 years ago)
Author:
gomidori
Comment:

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  • GOAnnotationGuidelines

    v10 v11  
    152152 * DNA binding
    153153  * for sequence-specific DNA binding, can use an annotation extension with 'occurs_at' and a SO ID (also see [#GOAnnotationExtensions] above)
     154 * Transcription factors - wherever possible (i.e. make exceptions only when data don't support this):
     155  * Remember to annotate to both a transcription factor activity term and a DNA binding term, because otherwise the TF won't be annotated to DNA binding, because the terms are connected by has_part in GO.
     156   * DNA binding: annotate to descendant of transcription regulatory region sequence-specific DNA binding (GO:0000976), e.g. RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978) is often the right one
     157   * Transcription factor activity: annotate to a descendant of sequence-specific DNA binding transcription factor activity (GO:0003700), usually RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077) or RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)
     158  * To capture target genes, put has_regulation_target extensions on the transcription factor activity term
     159  * Also put happens_during extensions on the TF activity term to capture stress, cell cycle phase, etc. No need to make redundant BP annotations.
    154160
    155161=== GO annotation and Redundancy ===