Changes between Version 32 and Version 33 of GOAnnotationGuidelines


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Timestamp:
Feb 25, 2015, 10:19:44 AM (6 years ago)
Author:
vw253
Comment:

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  • GOAnnotationGuidelines

    v32 v33  
    118118
    119119==== Molecular Function ====
    120  * Protein binding - annotate to GO:0005515 (or an allowable descendant) if there is enough information to conclude that there is a direct physical interaction. Otherwise just make BioGRID interaction annotation(s).
    121   * use IPI evidence; a 'with' entry is mandatory
    122   * note that GO:0019899 'enzyme binding' is in the do-not-annotate subset
    123   * we haven't (yet) tried to systematically delete older protein binding annotations that may not fit the direct interaction criterion
    124   * some protein binding annotations could presumably be inferred automatically from enzyme activity + input annotations (e.g. a protein kinase and a substrate identified in an extension)
    125  * DNA binding
    126   * for sequence-specific DNA binding, can use an annotation extension with 'occurs_at' and a SO ID (also see [#GOAnnotationExtensions] above)
    127  * Transcription factors - wherever possible (i.e. make exceptions only when data don't support this):
     120
     121  * Protein binding - annotate to GO:0005515 (or an allowable descendant) if there is enough information to conclude that there is a direct physical interaction. Otherwise just make BioGRID interaction annotation(s).
     122  * DNA binding  - for sequence-specific DNA binding, use an annotation extension with 'occurs_at' and a SO ID (also see [#GOAnnotationExtensions] above)
     123 
     124  * Transcription factors - wherever possible (i.e. make exceptions only when data don't support this):
    128125  * 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.
    129126   * 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