RefGenome10July07 Phone Conference (Archived)

Agenda

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

Present

• Rex Chisholm (dictyBase)
• Petra Fey (dictyBase)
• Pascale Gaudet (dictyBase)
• Sohel Merchant (dictyBase)
• Karen Christie (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)
• Ranjana Kishore(wormbase)
• Tanya Berardini (TAIR)
• Donghui Li(TAIR)
• Doug Howe (zfin)
• Susan Tweedie (flybase)
• Val Wood (Sanger- pombe)
• Victoria Petri (RGD)
• Chris Mungall (NCBO)

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

• Chris, Sohel and interested curators will have a separate conference call to discuss the tool

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)