RefGenome9Sept08 Phone Conference (Archived)

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  • Varsha Khodiyar
  • Ruth Lovering
  • Pascale Gaudet
  • Emily Dimmer
  • Kara Dolinski
  • Tanya Berardini
  • Donghui Li
  • Fiona McCarthy
  • Kimberly Van Auken
  • Ranjana Kishore
  • Mary Dolan
  • Chris Mungall
  • Seth Carbon
  • Amelia Ireland
  • Paul Thomas
  • Judy Blake
  • Stacia Engel
  • Jim Hu
  • Debbie Siegele
  • Li Ni
  • Rex Chisholm

Electronic Jamboree

Best date so far is Friday, Oct 10. Please vote by the end of this week (Sept 12)


  • Nothing much to report, still waiting for a new server at Berkeley (Seth)
  • When this is done, ref genome integration into AmiGO will be visible
  • This is also required for progress on the annotation progress tracker tool

Curation Targets

  • September 2008: Val's lists of 'unknowns'
  • Suggestions for October? Human group will provide targets

Discuss annotation issues

[ACTION ITEM]: Everyone should add to that wiki page how they use the response to terms (evidence codes and typical supporting experiment)

[ACTION ITEM]: Everyone who have comments about those issues should add them to the wiki pages. We'll discuss next month again and probably at the Montreal meeting.

Review old/ongoing action items

  1. Pascale: schedule electronic meeting in October [Done, kinda]
  2. Debby: Put in a SourceForge request that definitions of terms for oligomerization, dimerization, protein complex assembly etc. should be clarified as to their use and annotations using these terms be checked and, if necessary, changed.
  3. Emily and Debby: Clarify GO:0006730 one-carbon compound metabolic process and GO:0019438 aromatic compound biosynthetic process - these terms were added by the HAMAP and InterPro groups. Both of those processes involve enzymes that use a folic acid derivative as a coenzyme, but Debbie didn't think that FolE (which catalyzes the first committed step in folic acid biosynthetic) should be annotated to those processes.
  4. Susan: Request new term for Regulation of GTP Cyclohydrolase I activity. term requested
  5. Victoria: Make a SourceForge request to clarify the definitions of unfolded/misfolded protein binding and add chaperone activity as a synonym to both of the terms. Also add ‘de novo’ synonym to ‘unfolded protein binding’.
  6. Annotation_consistency:_HTP : Stacia SGD_GO_HTP_guidelines
  7. Annotation consistency: x protein binding and with : Becky, David
  8. Annotation consistency: Using IEP : Emily, Pascale, Ruth, Stacia
  9. Annotation consistency: 'Response to' terms Assigned to Tanya : Proper evidence code to use for to 'response to xx'? :Emily, Pascale
  10. All (ongoing): Annotation Quality control: Please pick an ortholog set from the Curation Targets table [1] see also Annotation_QC for some general documentation and previous issues
  11. All (ongoing): Annotation Quality control: Have a look at the SF items and see if the ortholog from your organism is correctly annotated ("comprehensive"). Let lead curator for that set know that you're done.

PPOD update

PANTHR update

Paul Thomas:

  • How to handle gp2protein files? in the context of alternative transcript, etc
  • Column 2 should have the unique 'canonical' gene; not every group has done that
  • Other issue is where would this file reside? 9somehwere on the GO site)
  • Rebuilding trees right now with the best data sets they managed to get
  • Should have something for everyone to look at before the GO meeting

Next conference call

Tuesday October 14, 2008, 10 AM CDT, 8 AM PDT, 4 PM BST

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