Difference between revisions of "RefGenome12Jun07 Phone Conference (Archived)"

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- Breath and depth metrics (Rex, Judy, Ruth)  
- Breath and depth metrics (Rex, Judy, Ruth)  
*'''Annotation consistency discussion''
*'''Annotation consistency discussion'''
- Karen: John Mullen annotation consistency study --we'll see if data is available
- Karen: John Mullen annotation consistency study --we'll see if data is available
- Kim: maybe hard to compare across such different organisms
- Kim: maybe hard to compare across such different organisms

Revision as of 07:52, 12 June 2007


  • Rex Chisholm (dictyBase)
  • Petra Fey (dictyBase)
  • Pascale Gaudet (dictyBase)
  • Karen Christie (SGD)
  • Eurie Hong (SGD)
  • Ruth Lovering (HGNC)
  • Fiona McCarthy (AgBase)
  • Judy Blake (MGI)
  • David Hill (MGI)
  • Harold Drabkin (MGI)
  • Mary Dolan (MGI)
  • Emily Dimmer (GOA)
  • Kimberly Van Auken (wormbase)
  • Donghui Li(TAIR)
  • Doug Howe (zfin)
  • Susan Tweedie (flybase)


  1. Discuss agenda items for meeting
  2. Plan to develop proposals for main issues on agenda
  • We should be able to have the meeting at Princeton after the GOC meeting
  • Strategies for identifying orthologs: Judy, Petra, Karen, DongHui and Kimberley

- now = YOGY, inparanoid, treefam
- one issue is about using consistent strategies
- we'd like to call in an expert at the meeting to help us
- Judy: orthology analysis: we want to have tools but we need to make sure we dont user-infer from that
- Rex: it's about specificity
- KarenC: different tools give different results; I'd like to know why and understand how those tools work
- Judy: I completely agree. We need to have by the meeting a white paper about how those tools work to provide a basis for discussion
- Kimberley: also noticed different results with different tools
- Emily: GAO has started to transfer electronic annotations; it's hard to keep track of the orthology information with different genome versions, especially for multispecies databases
- MaryD/David: we'd like to to produce a tool that would help make ISS annotations
- Emily: if this is automated, it should be IEA
- Rex: I think we should look at the superset of all the ref genome species (and do what??)

  • How to prioritize disease genes: Rex, Pascale, Emily

- Emily: will NCBI display that set of genes? This is a nice morbid map to provide and would give publicity
- Ruth: write a paper?
- Rex: important good addition
- Emily: do we have a target number of genes?
- Rex, Judy: all disease genes?
- Emily: do the genes have to be in morbid map?
- Pascale: if there is a paper, then it's a good target gene. Data must be convincing (not just expression)
- Judy: new ways to target new genes?

  • How to assess the progress made towards curation of reference genome genes; strategies for improvement (Rex, Karen, Emily, Susan

- We need to have a way to measure progress; right now it's rather crude. The data Rex sent last week was just counting how many genes each database has looked at. It included genes with no orthologs.
- David: We leave the lines with no orthologs blank.
- Rex: We had agreed to write it down that we checked
- We should have a monthly meeting and everyone would provide stats
- Synchronicity of curation: it would be more helpful if we were all curating at the same time - (a few) perhaps there are too many genes per month? - Rex: we discussed how many papers needs to be curated at the last GOC meeting (ie, we dont need to do everything)

  • Review of progress toward database and tool development (software group)

- Mary, Sohel, Chris will send a summary of what is being done - See

  • Discussions regarding metrics, including making a plan for how to use metrics

- Breath and depth metrics (Rex, Judy, Ruth)

  • Annotation consistency discussion

- Karen: John Mullen annotation consistency study --we'll see if data is available - Kim: maybe hard to compare across such different organisms (Pascale, Donghui?)

  • Karen E wants a gff3 file

- Judy: she wanted that for some tool development

  • inheriting annotations
  • web presence
  1. Review annotation stats.
  2. Regular monthly phone conference. Use to review stats, open ref genome source forge items
  3. Other issues? (no other issues)

Action items

Next meeting

Agenda for next reference genome conference call