Apr2007 ontology report

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Ontology Development & GO Editorial Office Report - April 2007

I. Ontology Development

  • SourceForge
    • Items opened: 80
    • Items closed: 66
      • GO Eds: 34
      • MOD curators: 15 (details in Appendix 1)
      • GO Ed/MOD collaborations: 17 (details in Appendix 2)
    • Items still open: 258
      • assigned, GO Eds: 48
      • assigned, MOD curators: 44
      • unassigned: 166
  • Work on the 'sensu' terms continues, and has extended into discussion of how GO should handle taxon information generally. Also, plant-related sensu terms have all been renamed, and work is now focused on mitotic spindle terms and insect terms. As before, detailed progress reports are available on the wiki (go to the Sensu main page and follow the 'Meeting Notes' link).
  • Collaboration with the Harvard/MIT GO Engineering group continues. GO developers (mainly David, Midori and Jane) have worked through the first set of "too specific" terms, and David has written up a summary of the discussion and changes we've made. Meanwhile, Mike Xiang has re-run the information content analysis looking at changes over time, especially before and after GO became is_a complete. Both sets of documents have been circulated among the active collaboration participants plus go-top, and can be made more widely available within GO.
  • Other content items resolved
    • Two-sector ATPase component terms (Midori)
    • Plant gametogenesis terms (Jen, Tanya, Donghui)
    • Various small things for SourceForge items
  • Other content items in progress
    • Many enzyme activity terms for img2go (Jane)
    • Resolving disjointness violations in the process ontology (Jane, using file of violations identified by Chris)
    • Regulation of process terms - check for consistency with process terms (David, using file from Chris)
    • Cross-products with ChEBI terms - conf call with ChEBI people planned
    • RNA processing (Karen C, Harold, Ceri) (addendum May 3, 2007)

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 released!
    • John has a prototype of OBO-Edit 2.0
    • Preparing abstract and paper to submit to Bio-ontologies SIG at ISMB
  • Software hub group (Jane, Amelia):
    • AmiGO working group (Jane, Amelia)
      • Continuing development to prepare for June AmiGO release
  • Advocacy group (Jane):
    • May newsletter in progress
    • Gohelp reorganized; now using google mail account
    • Some GO web site maintenance (Amelia)
    • Usual gohelp traffic
  • Annotation outreach (Jen) (note: much more detail in Jen's group report)
    • Jen and Emily on committee for chicken GO annotation and nomenclature (requested by Dave Burt at Roslin)
    • SOP discussions continuing; first flowchart, for ISS, available
    • Meeting & discussion with Astrid Meyer and some GOC people on possible cancer grant; Evelyn doing some writing
  • Conferences/meetings
    • Planning for muscle content meeting (Jen, Erika; see above)
  • Anything else
    • IMG mapping in progress (Jane)
    • figs2go mapping in progress (Jane)
    • Continuing work on ontology mapping tool, with Dietrich Rebholz-Schumann's group at EBI (Jane)
    • Also with Dietrich's group, collaboration on PubMed search tool (Jen)
    • GO Bibliography now has 1367 entries
Appendix 1: MOD curators' SF items
1686295 - David
1690792 - David
1690885 - Donghui
1693596 - David
1693852 - David
1697046 - David, Erika
1697093 - Donghui
1697103 - Donghui
1697132 - Donghui
1697188 - Donghui
1697190 - Donghui
1698622 - David
1704495 - Donghui
1706828 - Donghui
1708311 - Donghui

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1681353 - Rachael, community experts
1686839 - Nick
1686856 - Nick
1689328 - Karen C
1690789 - Tanya, Val
1693276 - Donghui
1694907 - Alex, Michelle
1695255 - Rama
1697124 - Donghui
1697147 - David, Tanya
1697231 - Kimberly, David
1697860 - Alex
1697904 - Alex
1700659 - Val
1702103 - Michelle
1702912 - Alex
1705933 - Val

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

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