RefGenome10Feb09 Phone Conference (Archived)

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Present

Pascale, Mike, Kimberley, Stan, Kara, Mary, Donghui, Stacia, Emily, Rachael, Susan, Suzi, Petra, Doug, Ruth, Li, Judy, Chris, Varsha, Lakshmi, Harold

PAINT software

  • hoping to have it available for this round of annotation
  • pulling data from the GO database (annotations)
  • need to write a GAF file

Next electronic jamboree Feb24

Please annotate genes !! Electronic_jamboree_feb24-2009


Annotation Issues

PAINT annotations: ISS

  • PAINT annotations are done in two steps:
    1. Annotating the common ancestor (hypothetical protein) by ISS by 'tree annotators'
    2. This generates a GAF file that can be used to propagate those annotations to all other descendants of that sequence
  • In both cases, the annotation uses ISS as evidence code. OK? YES
  • Step 1 : annotate ancestral sequence with ISS with all sequences with EXP data
  • Step 2 : annotate all other descendants with ISS with PANTHER ID

Qualifiers

  • Are they being used consistently and can we use them for propagation?

Contributes_to

  • Used with two different meanings: (1) when a multisubunit complex needs two or more gene products for activity, and (2) from documentation: "Note that contributes_to is not needed to annotate a catalytic subunit. Furthermore, contributes_to may be used for any non-catalytic subunit, whether the subunit is essential for the activity of the complex or not." [1]
  • This last statement should be removed. It's incorrect to annotate a function as if annotating a component.
  • contributes_to for RG genes (txt); File:Contributes to RG-2009-02.xls (xls)as of Feb 9, 2009:
  • Harold: this should be used only when it's absolutely required
  • sometimes get confused with regulation
  • Doug: should we carry the contributes_to when doing ISS?
  • Harold: for EXP: it depends on the experiment that was done

[ACTION ITEM]: fix documentation

Colocalizes with

  • Used with two different meanings: (1) transient localization, and (2) peripheral association.
    • Do we need to annotate peripheral associations? If the assay cannot resolve the component, should we not annotate to the parent?
    • If we mean 'transient', should the qualifier be 'transiently localized' (ie, more explicitly saying what we're trying to capture?
  • colocalizes_with for RG genes (txt); File:Colocalizes with RG-2009-02.xls (xls) as of Feb 9, 2009.
  • Emily: problem with many people use them differently so we have all this various data to go back and fix
  • Emily: should co-localizes be used for major terms such as leading edge, nucleus and cytoplasm (temporal sense)

[ACTION ITEM] (Emily): Send email to list to obsolete colocalises?? or remove the transient association meaning
[ACTION ITEM] (Pascale) generate lists of terms where it's been used

Fraction terms

  • From the TOP2 curation [[2]] : Should Fraction terms be obsoleted? Since they do not represent cellular components? If people agree here, we can ask the GO/annotation lists.
  • GO:0001950 : PME fraction
  • GO:0000267 : cell fraction
  • GO:0005625 : soluble fraction
  • GO:0005624 : membrane fraction
  • GO:0005626 : insoluble fraction
  • GO:0042598 : vesicular fraction
  • GO:0000299 : integral to membrane of membrane fraction
  • GO:0000300 : peripheral to membrane of membrane fraction
  • microsome

Next conference call

Tuesday March 10, 2009, 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST


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