Jan2007 ontology report

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Ontology Development & GO Editorial Office Report - January 2007

I. Ontology Development

  • SourceForge
    • Items opened: 94
    • Items closed: 74
      • GO Eds: 44
      • MOD curators: 21 (details in Appendix 1)
      • GO Ed/MOD collaborations: 9 (details in Appendix 2)
    • Items still open: 287
      • assigned, GO Eds: 80
      • assigned, MOD curators: 21
      • unassigned: 186
  • Plans firmed up for revamping the 'sensu' terms; work begins Feb. 1.
  • For the collaboration with Jonathan Liu et al. at MIT, we have scheduled a meeting for March 16th in Boston.
  • Funding for a muscle content meeting, to be held in Padua, Italy, has been confirmed by Giorgio Valle. Jen visited their group, and has put a plan on the wiki.
  • Other content items resolved
    • Further additions for PAMGO (Amelia, Jane, PAMGO curators)
    • Synaptic transmission terms (David)
    • Usual small things for diverse SF items
  • Other content items in progress
    • Making high-level process and component terms consistent
    • Continuing to clean up loose ends from is_a-complete process
    • Looking at phage ontology from Ariane Toussaint (Jane, with Michelle Gwinn)

David & Midori have set priorities for some tasks (several remain to be prioritized, but of those only a few are likely to be non-low priority), and added a draft timeline to the ontology development main page in the internal wiki.

There's also been a bit of progress towards a system for crediting community experts who contribute to ontology development; summary info is in manager call minutes and on the GO list.

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

  • OBO-Edit working group:
    • OBO-Edit 1.1 beta testing has had to continue, but is once again in a state of very-near-completion.
    • John has put a "roadmap" for OBO-Edit 2.0 development on the wiki.
  • Software hub group (Jane, Amelia):
    • AmiGO working group (Jane, Amelia)
      • "Silent" release - testing for move to new servers
      • Planning for release management
  • Advocacy group (Jane):
    • Website updates (Amelia)
    • RSC editor training (second session) (Jane, Jen)
  • Annotation outreach (Jen) (note: much more detail in Jen's group report)
    • Plant and Animal Genome Conference XV
    • Chicken and Cow Meeting - 22nd January in Cambridge, UK (Jennifer Clark and Evelyn Camon)
    • Visit to CRIBI at the University of Padua - 26th-27th January, Padua, Italy. (Jennifer Clark)(also relevant to content development)
    • TreeGenes database (http://dendrome.ucdavis.edu/treegenes) has expressed interest; TAIR would mentor.
  • Conferences/meetings
    • Jan. 2007 GOC meeting (all GOEs)
      • Post-meeting GO CVS and OBO-Edit tutorial session
    • Chicken and Cow Meeting - see above
  • Anything else
    • GO Bibliography now has 1217 entries
Appendix 1: MOD curators' SF items
1583186 - David Hill, David Fashena
1596553 - David
1609352 - Harold
1610130 - David
1610453 - Donghui
1611187 - Donghui
1611189 - Donghui
1611208 - Donghui
1614100 - Harold
1637893 - Karen C
1638895 - Karen C
1638928 - David
1642811 - Michelle
1642888 - Donghui
1642892 - Donghui
1642963 - Donghui
1644721 - Donghui
1644764 - Donghui
1644765 - Donghui
1644828 - Karen C
1647381 - David

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1438199 - Karen C, Pascale, Maria
1589414 - Harold, Rama
1605211 - David
1611196 - Donghui
1615195 - Doug
1623758 - David, Doug
1635881 - Alex
1635783 - Susan, Eurie, community expert Scott Hawley
1639638 - David

(Note: "MOD curator" is shorthand for any non-GO-Ed curator)

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