Changes between Version 83 and Version 84 of GOAnnotationGuidelines


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Timestamp:
Feb 25, 2015, 6:30:31 PM (6 years ago)
Author:
vw253
Comment:

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  • GOAnnotationGuidelines

    v83 v84  
    6262   *  When to make a GO process  annotation 
    6363      *   GO or phenotype  (update)
     64
     65 === Making GO process annotations from IMP ===
     66
     67We use GO annotations to describe direct involvement in a process, or its regulation (see below for more detail on regulation). We don't  annotate indirect upstream effects. Caution must therefore be used when using IMP to make process annotation, as it often isn't clear whether the effect is directly involved, regulation, or only affecting a process indirectly.
     68 
     69Often a number of phenotypes are used to make a GO annotation. [[BR]]
     70 
     71Example 1
     72 dil1 in /curs/c7fac5251ee4f493/ro/ where annotation to dynein-driven meiotic oscillatory nuclear movement with IMP is based on a combination of phenotypes :
     73 * decreased meiotic recombination
     74 * horsetail movement abolished
     75 * unequal meiotic chromosome segregation
     76 * decreased protein localization to microtubule cytoskeleton
     77
     78Example 2
     79 nda3 and mug164 annotations to intracellular distribution of mitochondria with IMP is based on
     80 * abolished mitochondrion inheritance
     81 * mitochondrial aggregation at cell tip
     82 * normal mitochondrial fission
     83 * normal mitochondrial fusion
     84
    6485 
    6586   * Regulation
     
    109130           * So I annotated pho7 to GO:0000978 (IPI with targets identified by ChIP-Seq) and GO:0001077 (IMP - Fig 4, plus can interpret Fig 2 ChIP-Seq as also supporting in light of Fig 4; have also thought about whether it might be good enough for IDA), with extensions on both to indicate phosphate starvation -- happens_during(GO:0016036) -- and the target genes highlighted in the text. In contrast, for csk1 I just used the BP GO:0045944 'positive regulation of transcription from RNA polymerase II promoter' with IMP. Full details in the [http://curation.pombase.org/pombe/curs/efb40309f7d22a73 curation session].
    110131 
    111 
    112 
    113132=== Gene Product Forms, or "Column 17" ===
    114133 
     
    118137
    119138=== GO supplementary IC (inferred from curator) annotation ===
     139
    120140  * Make any annotation (IC) which can be inferred by a curator but are not implicitly annotated by transitivity (i.e. because not included in the term ancestry). For example,
    121141  * [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0000808 origin recognition complex (ORC; GO:0000808)] subunits can also get:
     
    126146  * Also check whether any of these can be experimentally supported by data in the paper
    127147
    128 === Making GO process annotations from IMP ===
    129 
    130 We use GO annotations to describe direct involvement in a process, or its regulation (see below for more detail on regulation). We don't  annotate indirect upstream effects. Caution must therefore be used when using IMP to make process annotation, as it often isn't clear whether the effect is directly involved, regulation, or only affecting a process indirectly.
    131  
    132 Often a number of phenotypes are used to make a GO annotation. [[BR]]
    133  
    134 Example 1
    135  dil1 in /curs/c7fac5251ee4f493/ro/ where annotation to dynein-driven meiotic oscillatory nuclear movement with IMP is based on a combination of phenotypes :
    136  * decreased meiotic recombination
    137  * horsetail movement abolished
    138  * unequal meiotic chromosome segregation
    139  * decreased protein localization to microtubule cytoskeleton
    140 
    141 Example 2
    142  nda3 and mug164 annotations to intracellular distribution of mitochondria with IMP is based on
    143  * abolished mitochondrion inheritance
    144  * mitochondrial aggregation at cell tip
    145  * normal mitochondrial fission
    146  * normal mitochondrial fusion
    147 
    148 
    149148----
    150149[WikiStart Return to main page] or [CurationGuidelines Curation Guidelines]