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

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==Agenda==
 
==Agenda==
===Discuss agenda items for meeting===
+
==Discuss agenda items for meeting==
  
 
*We should be able to have the meeting at Princeton after the GOC meeting
 
*We should be able to have the meeting at Princeton after the GOC meeting
  
#'''Strategies for identifying orthologs'''
+
===Strategies for identifying orthologs===
 
* now = YOGY, inparanoid, treefam  
 
* now = YOGY, inparanoid, treefam  
 
* one issue is about using consistent strategies
 
* one issue is about using consistent strategies
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order of preference and pitfalls in identifying orthologs
 
order of preference and pitfalls in identifying orthologs
 
</pre>
 
</pre>
#'''How to prioritize disease genes'''
+
 
 +
===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<br>
 
- Emily: will NCBI display that set of genes? This is a nice morbid map to provide and would give publicity<br>
 
- Ruth: write a paper?<br>
 
- Ruth: write a paper?<br>
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</pre>
 
</pre>
  
*'''How to assess the progress made towards curation of reference genome genes; strategies for improvement (Rex, Karen, Emily, Susan'''
+
===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. <br>
 
- 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. <br>
 
- David: We leave the lines with no orthologs blank. <br>
 
- David: We leave the lines with no orthologs blank. <br>
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- Rex: we discussed how many papers needs to be curated at the last GOC meeting (ie, we dont need to do everything)<br>
 
- Rex: we discussed how many papers needs to be curated at the last GOC meeting (ie, we dont need to do everything)<br>
  
*'''Review of progress toward database and tool development (software group)'''
+
===Review of progress toward database and tool development (software group)===
 
- Mary, Sohel, Chris will send a summary of what is being done<br>
 
- Mary, Sohel, Chris will send a summary of what is being done<br>
 
- See wiki page<br>
 
- See wiki page<br>
  
*'''Discussions regarding metrics, including making a plan for how to use metrics'''
+
===Discussions regarding metrics, including making a plan for how to use metrics===
 
- Breath and depth metrics (Rex, Judy, Ruth) <br>
 
- Breath and depth metrics (Rex, Judy, Ruth) <br>
  
*'''Annotation consistency discussion'''
+
===Annotation consistency discussion===
 
- Karen: John Mullen annotation consistency study --we'll see if data is available<br>
 
- Karen: John Mullen annotation consistency study --we'll see if data is available<br>
 
- Kim: maybe hard to compare across such different organisms<br>
 
- Kim: maybe hard to compare across such different organisms<br>
 
(Pascale, Donghui?)
 
(Pascale, Donghui?)
  
*'''Karen E wants a gff3 file'''
+
===Karen E wants a gff3 file===
 
- Judy: she wanted that for some tool development
 
- Judy: she wanted that for some tool development
  

Revision as of 10:10, 12 June 2007

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

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 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??)
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

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: new ways to target new genes?

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

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 wiki page

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

Review annotation stats

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

  1. Alternate times: 8 AM/11AM CTD

Other issues? (no other issues)

Action items

Next meeting

Agenda for next reference genome conference call