RefGenome12Jun07 Phone Conference (Archived)

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Revision as of 10:24, 12 June 2007 by Pascale (talk | contribs) (4. Discussions regarding metrics, including making a plan for how to use metrics)

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Present

  • 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)

Agenda

Discuss agenda items for meeting

  • We should be able to have the meeting at Princeton after the GOC meeting

1. Strategies for identifying orthologs

  • 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, either Richard Durbin (pfam, treefam), Erik Sonnhammer (pfam, in paranoid), Paul Thomas (Panther)
  • Judy: orthology analysis: we want to have tools but we need to make sure we dont inappropriately infer information 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??)
ACTION ITEM: Judy, Petra, Karen, DongHui and Kimberley will write a write paper 
with an overview of how the different tools work, algorithm explanations, 
order of preference and pitfalls in identifying orthologs

2. How to prioritize disease genes

- 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 (~20,000)
- 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: Should we think of new ways to target new genes? including complex diseases

ACTION ITEM: Rex, Pascale, Emily will summarize the strategy used to identifying 
target genes and suggest possible improvements

3. How to assess the progress made towards curation of reference genome genes; strategies for improvement

- 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)

ACTION ITEM: Rex, Karen, Emily, Susan will write a list of information 
needed from curators to measure annotation progress 

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

ACTION ITEM: Rex, Judy, Ruth will summarize ideas on to how to capture 
breath and depth of annotations

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

ACTION ITEM: Mary, Sohel, Chris will send a summary of what is being done 
by the software group

- See wiki page


6. 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?)

7. Other points

  • Karen E wants a gff3 file

- Judy: she wanted that for some tool development.

  • inheriting annotations
  • web presence

Review annotation stats

Regular monthly phone conference. Use to review stats, open ref genome source forge items

  • Every second Tuesday of each month; alternate times: 8 AM/11AM Pacific time
  • Next meeting: Tuesday July 10, 1 PM CDT (11 AM PDT, 7 PM BST)

Other issues? (no other issues)=

Action items

Next meeting

Agenda for next reference genome conference call