RefGenome10Feb09 Phone Conference (Archived): Difference between revisions
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* Harold: this should be used only when it's absolutely required | * Harold: this should be used only when it's absolutely required | ||
* sometimes get confused with regulation | * sometimes get confused with regulation | ||
* Doug: should we carry the contributes_to when doing ISS? | |||
* Harold: it also sometimes depends on the experiment that was done | |||
===Colocalizes with=== | ===Colocalizes with=== |
Revision as of 12:32, 10 February 2009
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:
- 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? 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: it also sometimes depends on the experiment that was done
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.
Fraction terms
- From the TOP2 curation [[2]] : Should Fraction terms be obsoleted? Sine 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
Next conference call
Tuesday March 10, 2009, 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST
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