Changes between Version 68 and Version 69 of GOAnnotationGuidelines


Ignore:
Timestamp:
Feb 25, 2015, 5:55:21 PM (6 years ago)
Author:
vw253
Comment:

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  • GOAnnotationGuidelines

    v68 v69  
    5656  * sporulation ->ascospore formation  or children
    5757
     58 === GO annotation and Redundancy ===
     59
     60 If you are annotating a newer paper, and it repeats older well annotated experiments,  you do not need to capture the annotation.
     61
     62
    5863=== Biological Process ===
    5964
     
    9297=== Molecular Function ===
    9398   
    94    * Binding
    95    * [http://www.geneontology.org/GO.annotation.conventions.shtml#Binding_guidelines 'Binding' terms in MF]
     99 
    96100   * [http://wiki.geneontology.org/index.php/Annotation_consistency_:_ChIP_experiments chromatin immunoprecipitation (ChIP) experiments NOT promoter binding]
    97    * In !PomBase, we'll only annotate to a GO 'protein binding' term if there's strong evidence that a physical interaction is direct, e.g. using purified proteins. Otherwise, we'll just do the BioGRID interaction annotation.
    98   * 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).
     101   
     102  * Protein binding
     103    * In !PomBase, we'll only annotate to a GO 'protein binding'  GO:0005515  term if there's strong evidence that a physical interaction is direct, e.g. using purified proteins. Otherwise, just do the BioGRID interaction annotation.
     104    * We do not use gene product specific, or protein family specific, or GO function specific GO protein binding descendents (this would take  too long, and can be done with a query)
     105    * However we do use "domain specific' GO binding terms to specify binding toa specific region in a target protein
     106 
    99107  * DNA binding  - for sequence-specific DNA binding, use an annotation extension with 'occurs_at' and a SO ID (also see [#GOAnnotationExtensions] above)
    100108 
    101109  * Transcription factors - wherever possible (i.e. make exceptions only when data don't support this):
    102    * [http://wiki.geneontology.org/index.php/Transcription Transcription Overhaul details]
    103   * 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.
    104    * 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
    105    * 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)
    106   * To capture target genes, put has_regulation_target extensions on the transcription factor activity term
     110 
     111  * Remember  where possible to annotate to both a
     112     * transcription factor activity term  (sequence-specific DNA binding transcription factor activity (GO:0003700) or a descendent)  twith any target genes as has_regulation_target extensions and a
     113     * DNA binding term,  "transcription regulatory region sequence-specific DNA binding (GO:0000976)" or a descendent   (most commonly RNA polymerase II core promoter proximal region sequence-specific DNA binding GO:0000978) with any DNA binding motifs ar has_direct_input(SO:ID)
     114        *-otherwise the TF won't be annotated to DNA binding, because the terms are connected by has_part in GO).
     115   
     116  * To capture t on the transcription factor activity term
    107117  * Also put happens_during extensions on the TF activity term to capture stress, cell cycle phase, etc. No need to make redundant BP annotations.
    108118  * Example: [http://www.ncbi.nlm.nih.gov/pubmed/23231582 PMID:23231582] describes transcription during phosphate starvation. Mutations in pho7 or csk1 affect the -phosphate expression profile. For pho7 they also do ChIP-Seq and TAP assays, and some assays with a reporter construct, to establish that it acts as a transcription factor.
     
    112122   * The phenotypes themselves are another hairball, since they're mainly effects on global transcription measured by microarrays. In theory we could do annotations with extensions for all affected genes, but that would be insane. Try to get data for browser track; in meantime I'm just annotating to "altered RNA level during cellular response to phosphate starvation" without extensions. (2014-03-10)
    113123
    114 === GO annotation and Redundancy ===
    115 
    116  If you are annotating a newer paper, and it repeats older well annotated experiments,  you do not need to capture the annotation.
    117124
    118125=== Gene Product Forms, or "Column 17" ===