RefGenome11Sept07 Phone Conference (Archived)

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

Present

  • 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

We need to have some documentation ready for the meeting

  1. 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
  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.  

                                                                  --Kimberly
  1. 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
  2. Continue discussion on Outreach: publicizing the project and developing a web presence (lead by Susan and Rex)
  3. Continue discussion on Metrics: breath and depth of annotations (Rex, Judy, Ruth)

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)