Apr2008 ontology report

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Ontology Development & GO Editorial Office Report - March 2008

I. Ontology Development

  • SourceForge
    • Items opened: 76
    • Items closed: 67
      • GO Eds: 35
      • MOD curators: 14 (details in Appendix 1)
      • GO Ed/MOD collaborations: 18 (details in Appendix 2)
    • Items still open: 290
      • assigned, GO Eds: 59
      • assigned, MOD curators: 72
      • unassigned: 159 (Note: many of these will be closed on May 12, as agreed at the meeting)
  • Content items resolved
    • Sensu work completed!
    • Function-process pilot projects on electron transport, glycolysis, and TCA cycle reported at GOC meeting; links will be stored in spreadsheets or text files for the time being
    • Lipoprotein-related process and component terms - small collaboration with UCL and Reactome (Midori)
    • GO term-taxon pilot project presented at GOC meeting
    • Several SourceForge items resolved
  • Content items in progress
    • Follow-up to 'regulates' work continues, as noted last month.
      • Also, Jane looking at 'modulates' terms in light of 'regulates'
    • Function-process links for electron transport still being collected
    • Signal transduction overhaul continuing
    • Additional transport work continuing; new expert participant: Dr Paul Dobson, Manchester Interdisciplinary Biocentre
    • Various SourceForge items
  • IMG mapping update in progress (Antonio (EBI) has run mapping tool; Jane evaluating results)

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

  • Amelia is at Berkeley again
  • OBO-Edit working group:
    • More bug testing and documentation for OBO-Edit 2.0 (it never ends ...)
    • Jen's GUI for obomerge almost ready for testing
  • Advocacy/outreach
    • Annotation documentation added
    • AmiGO 1.6 - setting priorities
    • May newsletter in preparation
    • Discussion continuing with Steve Oliver on Aspergillus annotation jamboree
  • Meetings
    • GO Consortium meeting (Midori also at Reference Genome meeting)
  • Anything else
    • Chapter featuring GO and new AmiGO in "Bioinformatics for Tropical Disease Research: A Practical and Case-Study Approach" (Jane and Matt Berriman; http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=bioinfo.TOC&depth=2)
    • Work on InterPro2GO mappings for electron transport (Jen, with InterPro curators and electron transport wg)
    • GO bibliography has 1903 entries
Appendix 1: MOD curators' SF items
1902160 David
1906309 Karen C, Jim, Val
1912054 David
1913468 David
1934419 David
1943506 Tanya, David
1943514 Tanya, David
1943515 Tanya, David
1943518 Tanya, David
1943857 Tanya, David
1944041 Tanya, David
1944326 Tanya, David
1945401 Karen C
1954489 Tanya, David

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1219649 David, Pascale
1674020 many curators
1790306 Peter, Ruth
1846520 David
1852674 Peter, Ruth
1862215 Colin
1912842 several curators
1914443 David Sutherland
1922453 Peter
1924620 Peter, Stacia
1930727 Karen C
1933870 Karen C, Val
1938326 Karen C
1938334 Karen C
1939817 Chris
1942426 Karen C, Val
1943245 Karen C
1946205 Harold

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

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