Mar2008 ontology report

Ontology Development & GO Editorial Office Report - March 2008

I. Ontology Development

• SourceForge
  • Items opened: 56
  • Items closed: 48
    • GO Eds: 32
    • MOD curators: 4 (details in Appendix 1)
    • GO Ed/MOD collaborations: 12 (details in Appendix 2)
  • Items still open: 281
    • assigned, GO Eds: 56
    • assigned, MOD curators: 63
    • unassigned: 162

• Content items resolved
  • 'Regulates' relationships live (yay!) (David, Tanya, Chris, et al.)
  • Electron transport reorganization live (Jen and electron transport wg)
  • Sporulation terms reorganized (connected with the last of the sensu revamp, http://wiki.geneontology.org/index.php/Sporulation_Meeting_Notes)
  • Several SourceForge items resolved

• Content items in progress
  • Follow-up to 'regulates' work -- David and Tanya are still correcting errors reported by Chris' QC scripts; error reports will continue to be generated at least until OBO-Edit 2.0 is released (http://wiki.geneontology.org/index.php/Regulation_Main_Page).
  • Function-process pilot projects under way (http://wiki.geneontology.org/index.php/Function-Process_Links)
    • electron transport
    • glycolysis & TCA cycle (Harold)
  • Lipoprotein-related process and component terms - small collaboration with UCL and Reactome (Midori)
  • Signal transduction overhaul (Jen doing initial work and finding experts)
  • Additional transport work (Jen plus experts including Steve Oliver's group)
  • Initial exploration of plant processes affected by herbicides
  • Various SourceForge items

• IMG mapping update in progress (Jane)

• Switched to new go/ontology/directory structure ( Ontology_CVS_Directory_Layout_Overhaul )

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

• Jane's back!
• Amelia is preparing for another stint at Berkeley

• OBO-Edit working group:
  • More bug testing and documentation for OBO-Edit 2.0 (it never ends ...)
  • Jen contributing to programming (e.g. GUI for obomerge)

• Advocacy/outreach
  • AmiGO release to use 'regulates'
  • GO demo for WTGC master's students
  • Discussion with Steve Oliver on Aspergillus annotation jamboree

• Meetings
  • GO talk and AmiGO demo at EBI training roadshow, Ghent (Jen)
  • Workshop on "Making Small Facts Travel: Labels, Packages and Vehicles", London School of Economics (Midori)

• 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)
  • GO bibliography has 1876 entries

Appendix 1: MOD curators' SF items
1863992 David, Tanya
1912005 David
1929541 David
1929546 David, Tanya


Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1192485 Harold, Val
1807790 Jim
1881722 sporulation group
1894620 Peter
1898404 Chris, Alex, David
1901792 Karen C
1908887 Cindy
1909714 Rama
1911038 Alex
1911964 Rama, Val
1916944 Julie
1929533 Alex


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

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