RefGenome12Jun07 Phone Conference (Archived)

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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: GOA 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 orthologs identified by different tools and processes.
ACTION ITEM: Judy, Petra, Karen, DongHui and Kimberley will write a white 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. See Status of Reference Genome Project, June 5, 2007
- 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 [1] for Sohel's outline of use cases for the reference genomes database. He plans to have a prototype avaiulable in early July.
- Please be sure to consult the Reference Genome Database Requirements Discussion page [2] to add your input.

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
- Petra: Maybe we can look at a couple of specific disease genes that have been annotated and compare

ACTION ITEM: Pascale, Donghui will provide a framework for discussing 
consistency of annotations across genomes

7. Other points

  • Karen E wants a gff3 file

- Judy: she wanted that for some tool development.

  • inheriting annotations
  • web presence

Review annotation stats

See Status of Reference Genome Project, June 5, 2007

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