RefGenome10Feb09 Phone Conference (Archived): Difference between revisions
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===Qualifiers=== | ===Qualifiers=== | ||
* | * Are they being used consistently and can we use them for propagation? | ||
===Contributes_to=== | ===Contributes_to=== |
Revision as of 18:14, 9 February 2009
Present
PAINT software
Annotation Issues
PAINT annotations: ISS
- PAINT annotations are done in two steps:
- Annotating the common ancestor (hypothetical protein) by ISS by 'tree annotators'
- 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?
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:
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.
Next conference call
Tuesday March 10, 2009, 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST
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