RefGenome10July07 Phone Conference (Archived)

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


  • Rex Chisholm (dictyBase)
  • Petra Fey (dictyBase)
  • Pascale Gaudet (dictyBase)
  • Sohel Merchant (dictyBase)
  • Karen Christie (SGD)
  • Ruth Lovering (HGNC)
  • Varsha Khodiyar (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: Reference Genome meeting will be held 26 and the morning of the 27th in Princeton. Accommodations yet to be organized.


We will not have new targets for August. Use that time to catch up with annotations.

Review Action Items

ACTION ITEM 1: 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
  • An excellent review was just published in Ann Rev of Genetics by Kara Dolinski and David Botstein. This prvides the summary that we are looking for. Kara will give an overview and moderate the session at the Ref Genome Meeting. The reference is Annu. Rev. Genet. 2007. 41:465-507.

ACTION ITEM 2: Rex, Pascale, Emily will summarize the Strategy used to identifying target genes and suggest possible improvements

  • Current strategy is to use genes from the OMIM morbid map
  • There was a list of common genes between human, fly and zebrafish that was being used as a test case for PATO annotations; most of these genes were not used as they were not in the OMIM morbid map list
  • Suggestions: David, Emily others: it would be nice to focus on certain diseases rather than randomly pick genes involved in more or less medically important diseases
  • Judy has another list with disease genes common between human, mouse and [??]
  • Victoria: RGD has several lists of genes implicated in various types of diseases, such as cardiovascular, neurological diseases
  • Ruth: focusing on specific diseases would give more direction to the project and make its justification easier
  • Judy: we could chose a disease and one person could read a review and send a list of all relevant genes
  • Rex: let's do that for the next few months and see how it works

ACTION ITEM 3: Rex, Karen, Emily, Susan will write a list of information needed from curators to measure Annotation progress

  • Curators feel that 'completely' curating a gene is often impossible (when there is too much literature). We will now refer to 'curation status = comprehensive' rather than complete. This means that the curator feels the annotations for that gene represent well the status of the knowledge regarding the gene's function, process, component.
  • The column currently labeled 'Date completed' in the individual spreadsheets should be renamed "Curation comprehensive as of (MM-DD-YYYY)
  • Other stats can be derived from the total number of publications, number of publications chosen for GO, and number of papers curated

ACTION ITEM 4: Rex, Judy, Ruth will summarize ideas on to how to capture Metrics: breath and depth of annotations
ACTION ITEM 5: 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

  • Chris, Sohel and interested curators will have a separate conference call to discuss the tool
  • Karen wanted to know where the reference genome database was to be held; we don't know that yet

ACTION ITEM 6: Pascale, Donghui will provide a framework for discussing Consistency of annotations across genomes

  • Pascale: Maybe the title of this one was incorrect. The idea is to compare annotations to do some 'quality control' to remove incorrect information and also to add information if one of the curated orthologs is missing any.
  • One suggestion is to assign genes to curators and that curator would check all annotations and make suggestions if necessary.
  • Another suggestion was for curators to 'claim' genes as they curate them
  • Rex and Pascale will send a list of genes for to each curator to review
  • Some objections (Doug, others): this may be a lot of work. Also, there must be ways to automate that.
  • Judy: we should use Mary's graphs
  • Mary: those will be updated
  • Karen: cannot find the graphs easily.
  • Rex: The link used to be there from the reference genome wiki page, seems to be missing (need to add those back; is it ? )

ACTION ITEM 7: Susan and Rex will present suggestions for Outreach: publicizing the project and developing a web presence

  • There are some suggestions in the wiki page from Emily, Susan and Ranjana
  • Not really discussed, we'll discuss more next time

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?

New action items

  1. 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
  2. RG software group and some curators will have a phone conference to discuss the new tool
  3. Annotation consistency/ quality control: Rex and Pascale will send all the curators on the RG mailing list a list of genes to verify; we'll see how it goes and discuss next time
  4. Continue discussion on Outreach: publicizing the project and developing a web presence (lead by Susan and Rex)
  5. Continue discussion on Metrics: breath and depth of annotations (Rex, Judy, Ruth)

Next meeting

Tuesday August 7, 10 AM CDT (8 AM PDT, 4 PM BST)
Agenda: RefGenome07Aug07_Phone_Conference.doc