Aug2008 ontology report

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Ontology Development & GO Editorial Office Report - August 2008

I. Ontology Development

  • SourceForge
    • Items opened: 114
    • Items closed: 123
      • GO Eds: 70
      • MOD curators: 35 (details in Appendix 1)
      • GO Ed/MOD collaborations: 18 (details in Appendix 2)
    • Items still open: 259
      • assigned, GO Eds: 73
      • assigned, MOD curators: 97
      • unassigned: 89
  • Content items resolved
    • peptidase MF terms - high-level terms organized; gene-product terms obsolete (Midori, Colin, Peter, Ben, Darren Natale, MEROPS)
    • Several SourceForge items resolved
  • Content items in progress
    • Regulates relationships within MF and between MF and BP are planned, and have been announced (David, Tanya)
    • additions (Jane, with PAMGO curators)
    • Processes affecting cellular components (Jane, David, Midori, Val, et al.)
    • Signal transduction overhaul continuing, with high-level terms now in place; latest notes at Signaling_Meeting_Minutes_April_2008_- (Jen, David)
    • File of triggers for annotation QC - first set based on applicability will be tested by Ensembl (EBI) programmers; previously reported as taxon links (Jen, Chris)
    • Regulates relationships for multi-organism processes (Jane)
    • Function-process links for electron transport, metabolic pathways (Jen, Harold, et al.)
    • Red light/fluence terms - file in scratch directory (Jen)
    • Quality control reports generated by Chris
      • Regulation (David, Tanya)
      • Many others to be dealt with; we've made a start on multiple part_of parents (several GO curators)
    • Various SourceForge items

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

  • Amelia at Berkeley
  • OBO-Edit working group:
    • OBO-Edit 2 testing and documentation
    • Configuration system updated for Graphviz Viewer and Tree Viewer (Jen)
  • Advocacy/outreach
    • August newsletter released
    • AmiGO 1_5_2_2 now in production
    • Usual gohelp traffic
  • Publications
    • AmiGO manuscript in preparation (AmiGO/web presence wg)
  • Meetings
    • OBO Foundry meeting July 7-8 (Jane)
    • High Throughput Cell Based Screening Workshop, July 17-18 (Midori)
  • Anything else
    • GO bibliography has 2090 entries
Appendix 1: MOD curators' SF items
981451 David, Michelle, Rama
1187644 David, Pascale
1388826 David
1459158 David, Doug, Erika
1472252 David
1629027 David
1766338 David, Doug, Michelle
1940087 David, David OS
1955525 David, Tanya, David OS, Susan
1968619 Tanya, David
1986235 Tanya, David
1990110 Tanya, David
2012941 Donghui
2013833 Tanya
2013886 Donghui
2013895 Donghui
2013902 Donghui
2015841 Tanya, David
2016145 Tanya, David
2021843 Tanya, David
2023398 Tanya, David
2030820 Donghui
2031961 Donghui
2031970 Donghui
2031980 Tanya
2034198 Donghui
2039409 David
2040801 Harold
2044782 Tanya
2048702 Tanya
2053749 David, Tanya
2053758 Donghui
2053765 Donghui
2059033 David
2074156 Harold

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1226219 peptidase wg
1439673 David, Harold
1441782 Alex, David
1515279 David
1561376 Tanya, David
1943157 peptidase wg
1943255 peptidase wg
1953281 Val, Julie
2019054 Debby
2023928 Peter
2027305 David, Tanya
2029645 David
2034849 Rama, John Garavelli
2034960 Tanya, David
2035166 Rama
2043737 Colin
2062881 Rama
2068235 Alex

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

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