RefGenome11Sept07 Phone Conference (Archived)

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Tuesday September 11, 2007, 1 PM CDT (11 AM PDT, 7 PM BST)


  • Petra Fey (dictyBase)
  • Ruth Lovering (HGNC)
  • Judy Blake (MGI)
  • David Hill (MGI)
  • Harold Drabkin (MGI)
  • Emily Dimmer (GOA)
  • Kimberly Van Auken (wormbase)
  • Donghui Li(TAIR)
  • Susan Tweedie (flybase)
  • Val Wood (Sanger- pombe)
  • Victoria Petri (RGD)
  • Chris Mungall (NCBO)
  • Suzi Lewis
  • Rex Chisholm (dictyBAse)
  • Doug Howe (ZFIN)
  • ??? (SGD)

Discuss meeting agenda

Judy-suggested restructure of the Ref Gen meeting agenda to accommodate a conference call with other PIs involved in the genome Resource Informatics Network (GRIN).

Proposed Agenda Update:

Morning of the 26th

  * Orthology discussion (moderated by Kara Dolinski)

Noonish on the 26th

  * Conference call with the GRIN PIs to discuss conservation of effort, orthology sets, sharing data.

Afternoon on the 26th

  *priorities (moderated by Rex and Pascale)
     How should new genes be chosen?   
  *methods (moderated by Suzi, Judy expounds)
     Complete vs. comprehensive annotation issue. 
     What is our goal:
         'complete' annotation of 500 genes"
         'comprehensive' annotation of 1000 genes?
         'good' annotation of 2000 genes?
  *metrics (moderated by Ruth)
     How do we assess completeness, comprehensiveness, breadth and depth??
  *tools (Moderated by Chris with assist from Mary)
     Discussion of software to assist in RG project

Morning of the 27th

  * annotation consistency (moderated by Pascale)
  * promotion of resource (moderated by Susan)
      -publication, website, etc.

Review Action Items

  • Judy, Petra, Karen, DongHui and Kimberley summarize how the different Tools for identifying orthologs work, algorithm explanations, order of preference and pitfalls in identifying orthologs (DONE)
  Would it also be helpful to have groups present 1-2 of their more difficult ortholog assignment cases at the Princeton
  meeting so that we can attempt to draw up some guidelines for how to handle these cases?
  I'd be willing to collect and collate these before the meeting.  

  • Annotation consistency/ quality control: Rex and Pascale will send all the curators on the RG mailing list a list of genes to verify; we'll see how it goes and discuss next time. See example ATPAF2
-There was concern among the group about doing it didn't happen since last meeting.  

Rex/Pascale will send out a small list of genes to the group for examination ASAP so they can be reviewed before the RG meeting. Bring comments on utility of this effort to the RG meeting.

 -No discussion took place in phone conf.  Susan will lead discussion at RG meeting.
-Suzi will lead discussion at RG meeting, Judy will expound.
-Harold-How will we handle the indication that a gene is curated "comprehensively"?
       -How will that "comprehensive" status be kept up to date?
       -How will we know when a gene should lose it's "comprehensive" curation satus?
-Rex-Revisiting curation of "comprehensive" genes will become an increasing curation burden 

as time goes on. How can we mitigate that?

-David-Some genes acquire new pubs much more quickly than others, focus effort on genes with most new pubs?
      -We currently spend a lot of time updating the spreadsheets, need to find a way to mitigate the bean counting effort ASAP.

Curation Targets

  • If all goes according to plan, those should have been selected from the RGD neurological disease list.
  • Any comments?

Reference genome curation tool update

Next meeting

Tuesday October 16, 10 AM CDT (8 AM PDT, 4 PM BST)