Aug2007 ontology report

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Ontology Development & GO Editorial Office Report - August 2007

I. Ontology Development

  • SourceForge
    • Items opened: 78
    • Items closed: 93
      • GO Eds: 58
      • MOD curators: 14 (details in Appendix 1)
      • GO Ed/MOD collaborations: 21 (details in Appendix 2)
    • Items still open: 268
      • assigned, GO Eds: 54
      • assigned, MOD curators: 48
      • unassigned: 166
  • Other content items in progress
    • Quite a bit of progress on sensu terms; plan established to deal with last remaining ones; see http://gocwiki.geneontology.org/index.php/Meeting_Notes_3
    • David is working through Chris' file of "regulation of non-process" anomalies; in some cases, new process terms are needed, and in other cases regulation terms need to be moved under regulation of molecular function or regulation of biological quality
    • Many synonyms for enzyme activity terms added, derived from EC via Expasy; an update/refinement based on IntEnz is on the way
    • Resolwing a few disjoint violations that have cropped up (mainly David, also GO Eds)
    • Various SourceForge items

See monthly report in CVS for ontology statistics.


II. GO Editorial Office activities not represented in part I

  • OBO-Edit working group:
    • Additional OBO-Edit 2.0 betas released; new search/filtering interface in progress
  • Software hub group (Jane, Amelia):
    • AmiGO working group (Jane, Amelia)
      • Continuing development to prepare for next AmiGO 1.0 release
  • Advocacy group (Jane):
    • Slides for general GOC use (continued)
    • August newsletter released
    • Usual gohelp traffic
  • Annotation outreach (Jen) (note: much more detail in Jen's group report)
    • Continuing work on SOPs
  • Conferences/meetings
    • Interactome Networks in progress (Aug. 30-Sept. 1; Jen, Ben)
  • Anything else
    • NAR database issue manuscript in progress (content: GO managers; submission: Midori)
    • FIGS2GO mapping - about 1000 terms (Jane)
    • Parasite book chapter revisions (Jane, with Matt B)
    • GO Bibliography now has 1549 entries
Appendix 1: MOD curators' SF items
780275 Harold, Karen C, Ceri
1067017 Harold, Karen C, Ceri
1566692 Harold, Karen C, Ceri
1711527 Donghui
1711561 Donghui
1732986 Donghui
1716772 Donghui
1771261 Donghui
1773245 Donghui
1773281 Donghui
1773295 Donghui
1773312 Donghui
1773238 Tanya
1744496 Tanya


Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1322372	Pascale, Val
1759080	Val
1759812 David
1762047 Jodi, Val
1105967 John G
1729099 Harold, Karen C, Peter d'Eustachio
1757389 Val
1450780 transporter wg
1728089 Karen C, Val
1766694 Karen C, Val
1768428 Rama, Val
1767388 Karen C
1770519 Rob
1769547 David
1771167 Rama
1771174 John G
1727804 transporter wg
1778477 Karen C
1778468 Tanya
1744395 Tanya, Jim Hu
1488957 Tanya

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

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