Managers 06May09

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Agenda/chair: Midori
Minutes: Pascale
Present: Midori, Jen, Jane, Pascale, David, Chris, Judy

Action items from previous calls

All are carried over from March 25

  • Pascale and Jane: Organize conference call on usage of tricky GO terms; include ontology editors and annotators (both ref gen and broader annotation list). -> We'll try to do something for the June Reference genome conference call, June 9th.
  • Pascale, Chris: Finish and circulate gp2protein file documentation. IN PROGRESS
  • PIs will discuss Jen's funding situation and get back to Jen immediately. (Current contract finishes 14th July.)

Discussion items

  • Jennifer is very close to finishing the implementation of the trigger file for annotation checking, and to being able to strip out the sensu synonyms from the live file. If this can be done in time, she would like to write up the project and submit it as a paper to the IEEE International Conference on Bioinformatics and Biomedicine (BIBM09), Washington DC, USA, Nov. 1-4, 2009. Getting this published might be very helpful in looking for future funding opportunities. Would there be any objection to submission of this paper? Time is getting a bit tight, so if no objections are lodged at this meeting, she will assume it is okay to proceed.

[Action item] Jen will send a plan: bullet points and an abstract to GO-tops and Chris describing what the paper will be. Where to submit this needs to be discussed. Maybe we should consider a real journal rather than conference proceedings.

  • Amelia has suggested that we get a logo professionally designed for GO. She suggested this website: Basically you put up a brief for the logo and an amount of prize money (between 100 and 600 USD) and people submit designs. After a week you choose one and the winner gets the prize money. [Jane]

[Action item]: Jane: Ask GO-tops about getting a logo professionally designed for GO

  • Papers:
  • In progress:
    • Book chapter on ontology development, GO-style: David, Judy, Tanya, Chris
    • Review for MR&D on using go to study development: David, Tanya, Doug and Kimberly
    • Invitation from the new journal DATABASE for papers from the Biocurators conference (deadline May 31st) - should we submit a paper about 'regulates' (Midori's poster)? [David, Midori, Jane, Chris, Tanya]
    • Ideas from Chris, in rough order of priority
      • regulation in the GO - genome biology : TO BE DONE NOW - Jane & Midori
      • xps in the GO, general - extension of the ICBO paper
      • cellular processes
        • fold in to the above?
        • include Val, discussion of term enrichment when using pre-composed mt translation terms etc
      • treatment of multi-organism processes in the GO - could be folded into a more general paper about treatment of symbiosis across the obo foundry
      • new spatial relations in CC - could be a collaboration with anatomy ontology folks
      • GO and organismal taxonomy
      • GO, development, anatomy, CL xps - include uberon, Melissa
  • F-P links have gone live. We should talk about the plan to continue this and how we will feed annotations back to the refgenome group.
  • Reference genome: Some people have asked Pascale to participate in the reference genome group: rice (not sure how serious they were) and a group in Montreal working on Aspergillus. The Aspergillus annotations (if well done) could be interesting because they would mostly cover groups of genes we're done doing (catabolism). How could we incorporate this data?
    • Judy: There is no reason not to include other groups that want to provide annotations.

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