RefGenome11Sept07 Phone Conference (Archived)

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

Present

  • Judy Blake (MGI)
  • David Hill (MGI)
  • Harold Drabkin (MGI)
  • Emily Dimmer (GOA)
  • Kimberly Van Auken (Wormbase)
  • Ranjana Kishore (Wormbase)
  • Donghui Li(TAIR)
  • Tanya Berardini (TAIR)
  • Susan Tweedie (flybase)
  • Val Wood (Sanger- pombe)
  • Victoria Petri (RGD)
  • Chris Mungall (NCBO)
  • Seth Carbon (BBOP)
  • Suzi Lewis
  • Rex Chisholm (dictyBase)
  • Doug Howe (ZFIN)
  • Stacia Engel (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 Previous 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.  

                                                                  --Kimberly
  • 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 this..so 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.
 -Susan will lead discussion at RG meeting.
-All of us should keep eyes open for interesting RG genes that provide unique insight or are
particularly informative to enhance the soon to be written RG publication.
-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 spend a lot of time updating the spreadsheets, need to find a way to mitigate the bean counting effort ASAP. -Judy-'Hot' genes (being published on currently) need more attention than 'cold' genes.

Curation Targets

  • September list was from the RGD Neurological Disease List
 David-this list produced many more publications to curate than past lists for MGI
 Doug-this list was no different for ZFIN than any other
 SGD-No orthologs were identified for this set.  Raised concern that 
     continued use of similar lists will minimize the contribution from more distantly related organisms.

Reference genome curation tool update

  • No curation tool updates to report

Rex-New developer has been hired to start in Nov. -Chris should talk to Erik re: Sohel's software

Judy-Harold has updated Mary's graphs to reflect all genes through the July set.
-The main change was the inclusion of the GOSlim comparison matrix

 http://www.geneontology.org/images/RefGenomeGraphs/

-Chris/Mary to discuss incorporation of refG_target and orthology info in db, integration with AmiGO at upcoming GO meetings

New Action Items

-Incorporate Ruth's document into the wiki (Judy)
-Send out a small set of genes to RG list for review as was done for ATPAF2 gene noted above. Provide info on how review is to be done...(Rex/Pascale)

Next meeting

Tuesday October 9, 10 AM CDT (8 AM PDT, 4 PM BST)