RefGenome10Feb09 Phone Conference (Archived)

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Present

PAINT software


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?


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.

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?


Next conference call

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


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