RefGenome10July07 Phone Conference (Archived): Difference between revisions

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4. ACTION ITEM: Rex, Judy, Ruth will summarize ideas on to how to capture [[Metrics: breath and depth of annotations]]
4. ACTION ITEM: Rex, Judy, Ruth will summarize ideas on to how to capture [[Metrics: breath and depth of annotations]]
5. ACTION ITEM: Mary, Sohel, Chris will send a summary of what is being done by the [[RG Software group]]
5. ACTION ITEM: Mary, Sohel, Chris will send a summary of what is being done by the [[RG Software group]]
* There is a test server available since this morning
<pre>
[http://rails-dev.bioinformatics.northwestern.edu:24000/curator]
[http://rails-dev.bioinformatics.northwestern.edu:24000/admin]
</pre>
6. ACTION ITEM: Pascale, Donghui will provide a framework for discussing [[Consistency of annotations across genomes]]
6. ACTION ITEM: Pascale, Donghui will provide a framework for discussing [[Consistency of annotations across genomes]]
7. ACTION ITEM: Susan and Rex will present suggestions for [[Outreach: publicizing the project and developing a web presence]]
7. ACTION ITEM: Susan and Rex will present suggestions for [[Outreach: publicizing the project and developing a web presence]]

Revision as of 15:34, 10 July 2007

Agenda

Tuesday July 10, 1 PM CDT (11 AM PDT, 7 PM BST)

Reference Genome meeting update

Judy: will be held 26 and the morning of the 27th in Princeton. Accommodations yet to be organized.

Review Action Items

1. ACTION ITEM: 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

  • Judy was away last week, this will be done for the next meeting

2. ACTION ITEM: Rex, Pascale, Emily will summarize the Strategy used to identifying target genes and suggest possible improvements 3. ACTION ITEM: Rex, Karen, Emily, Susan will write a list of information needed from curators to measure Annotation progress 4. ACTION ITEM: Rex, Judy, Ruth will summarize ideas on to how to capture Metrics: breath and depth of annotations 5. ACTION ITEM: Mary, Sohel, Chris will send a summary of what is being done by the RG Software group

  • There is a test server available since this morning
[http://rails-dev.bioinformatics.northwestern.edu:24000/curator] 

[http://rails-dev.bioinformatics.northwestern.edu:24000/admin]

6. ACTION ITEM: Pascale, Donghui will provide a framework for discussing Consistency of annotations across genomes 7. ACTION ITEM: Susan and Rex will present suggestions for Outreach: publicizing the project and developing a web presence

Annotation Progress

  • How many of the human genes have orthologs identified ?
  • How many of these have papers associated (are published genes) ?
  • How many papers associated in total ?
  • How many papers have been considered for GO curation ?
  • How many papers provided GO terms ?
  • How many genes which have papers associated are considered complete/comprehensive ?

Issues with target genes

  • pombe (Val): takes a long time to triage papers
  • GOA, pombe: too many genes per month
  • If too many groups are falling behind, we should consider skipping August
  • not enough coordination between annotation efforts
  • pombe/dictyBase: We would like to know when other databases have completed annotation

- Judy suggestion: Change from 'complete' to 'comprehensive'
- Pascale: did we not have a wiki for doing that?


Next meeting

Tuesday August 14, 10 AM CDT (8 AM PDT, 4 PM BST)