RefG Princeton April 12-13 2010: Difference between revisions

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* Very useful to spend a few minutes looking at a review, geneWiki, etc for an overview of the family when PAINT curators are not familiar.
* Very useful to spend a few minutes looking at a review, geneWiki, etc for an overview of the family when PAINT curators are not familiar.
* Use ortholog mapping to do a reality check on the tree: 1) overall look, see if OrthoMCL makes sense.  If it does not, contact Paul and the tree will be edited as appropriate.
* Use ortholog mapping to do a reality check on the tree: overall look, see if OrthoMCL makes sense.  If it does not, contact Paul and the tree will be edited as appropriate.
* Start with Mol. Function, Cell Component, Biol. Process


=Misc Notes=
* Enable the ability to say "do not propagate" to a particular clade, distinguished from adding an explicit NOT, for example, based on long branch/rapid divergence





Revision as of 11:29, 12 April 2010

Propagation Rules/SOP

  • Very useful to spend a few minutes looking at a review, geneWiki, etc for an overview of the family when PAINT curators are not familiar.
  • Use ortholog mapping to do a reality check on the tree: overall look, see if OrthoMCL makes sense. If it does not, contact Paul and the tree will be edited as appropriate.
  • Start with Mol. Function, Cell Component, Biol. Process

Misc Notes

  • Enable the ability to say "do not propagate" to a particular clade, distinguished from adding an explicit NOT, for example, based on long branch/rapid divergence


Monday 4/12

Rm 280 10am-1pm.

Quick tour for new PAINT users (Li and Mary): Ed gave a quick tour of the latest version of PAINT.

Review protein families, see: http://wiki.geneontology.org/index.php/GAFs_for_trees-based_annotations While reviewing protein families, we can generate a list of propagation rules. We can pick up lunch in our cafe, and work through lunch.

LONP1/2


CPS

HPRT


Rm 253 1pm-4pm.

Continue to review protein families. Refine the list of propagation rules after a day's worth of reviewing families.

Tuesday 4/13:

Rm 253 10am-11am

GO annotation camp discussion

Rm 280 11am-1pm

Working lunch to go over misc. discussion items:

  • (Pascale): Should we remove GO:0005515 (protein binding) form the list of terms we see in PAINT?
  • (Mike): Is the PANTHER to P-POD OrthMCL mapping currently working?
  • (Mike): Should we fix the dates in the new GAF files to reflect when the annotations were actually made?
  • (Mike): Could we re-generate the statistics from the GAF files using a script (rather than manually)?
    • Probably easy enough, once we discuss what stats we're interested in capturing (Ed)
  • (Mike): Pascale noticed a problem with the literature linkouts to Wormbase, and I just had some trouble with ZFIN
    • Fixed (Ed)


Rm 253 1pm-4pm

Annotation tracker: Sven, CJM, Seth

  • Current issues/roadblocks
  • Subfamily issue: can we deal?
  • Feedback
  • Can we leverage the annotation reporter to generate the monthly lists in an easier way?

Paper

  • Title: ???
  • Authors: as on this mailing list, and possibly adding CJM, Seth, and Sven if we add a section on the DB and the other GO-top PIs
  • Affiliations: obviously
  • Abstract: Paul?
  • Author Summary: Suzi will take a crack at this
  • Introduction: Pascale&Paul
  • Results: as below, with possible addition of DB section and web interface, although this could be a different paper. Ed and Suzi can write #1, Paul&Mike for #2?
  • Discussion: #3 (Mike & Kara)
  • Materials and Methods: cut and dry, write at the end
  • Acknowledgments: all the curators at the MODs, the grant...
  • References, Figure Legends, Tables: as they fall out from the above.