Changes between Version 90 and Version 91 of GOAnnotationGuidelines


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Timestamp:
Nov 5, 2015, 10:37:05 AM (5 years ago)
Author:
mah79
Comment:

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  • GOAnnotationGuidelines

    v90 v91  
    102102 * DNA binding - for sequence-specific DNA binding, use an annotation extension with 'occurs_at' and a SO ID (also see [#GOAnnotationExtensions] above). The rationale is that the bound substrate is the whole DNA molecule, and the SO extension indicates the region where binding takes place.
    103103  * If you don't know whether a gene product is binding to DNA or protein (or both) in chromatin, you can use "chromatin binding" again with 'occurs_at(SO:nnn)' extensions ... BUT:
    104   * Don't use "promoter binding" terms if the only evidence is chromatin immunoprecipitation (ChIP). In fact, it's safer not to use a binding term at all; use a "chromatin" cellular component term instead. See the [http://wiki.geneontology.org/index.php/Annotation_consistency_:_ChIP_experiments GO wiki page on ChIP experiments]. Specify where with 'coincident_with(SO:nnn)' or ''coincident_with(PomBase:id)' extensions.
     104  * Don't use "promoter binding" terms if the only evidence is chromatin immunoprecipitation (ChIP). In fact, it's safer not to use a binding term at all; use a "chromatin" cellular component term instead. See the [http://wiki.geneontology.org/index.php/Annotation_consistency_:_ChIP_experiments GO wiki page on ChIP experiments]. Specify where with 'coincident_with(SO:nnn)' or 'coincident_with(PomBase:id)' extensions.
    105105 * Transcription factors - wherever possible make annotation to both:
    106106  * 1. a transcription factor activity term (sequence-specific DNA binding transcription factor activity (GO:0003700) or a descendant) with any target genes as has_regulation_target extensions, and optionally a promoter in an occurs_at(SO:nnn) extension; and a