Jan2008 ontology report

Ontology Development & GO Editorial Office Report - January 2008

I. Ontology Development

• SourceForge
  • Items opened: 97
  • Items closed: 111
    • GO Eds: 63
    • MOD curators: 22 (details in Appendix 1)
    • GO Ed/MOD collaborations: 26 (details in Appendix 2)
  • Items still open: 285
    • assigned, GO Eds: 46
    • assigned, MOD curators: 68
    • unassigned: 171

• Content items resolved
  • Improved relationships for regulation terms (see below)
  • Several SourceForge items resolved

• Content items in progress
  • LOTS of progress on regulation! Chris, David and Tanya have made numerous improvements in the "live" GO file to add missing relationships, correct errors, and move regulation terms to more specific parents, all using the existing is_a and part_of relationship types. They have also sent an email announcing the date -- March 25, 2008 -- when GO will deploy the 'regulates' relationship. As always, much more information is available on the wiki (http://gocwiki.geneontology.org/index.php/Regulation_Main_Page).
  • Sensu revamp almost done - proteasome, ribosome, cell wall and other changes now live; only a few things left on the to-do list (http://gocwiki.geneontology.org/index.php/Meeting_Notes_3)
  • Transport/transporter work resuming
  • Lipoprotein-related process and component terms - small collaboration with UCL and Reactome
  • Various recombination-related process terms
  • Various transcription-related process terms
  • Various SourceForge items

• Erika and Jen have written a manuscript on the muscle content meeting, and will try to submit it to a muscle journal; backup plan would be a bioinformatics journal

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

• Jane on maternity leave

• OBO-Edit working group:
  • Continuing to focus on updating documentation for OBO-Edit 2.0
  • On the lighter side, designing icons for the 'regulates' relationship

• Advocacy/outreach reported to GO managers (http://gocwiki.geneontology.org/index.php/Managers_30Jan08). Highlights:
  • Plans for avian annotation meeting
  • GO tutorial in preparation for use in EBI "roadshows"
  • Negotiations with OpenHelix on proprietary training material for GO

• Anything else
  • GO bibliography has 1772 entries

Appendix 1: MOD curators' SF items
1073890 Becky, Doug, Russ
1371173 David
1583546 Val, Maria
1758855 Eurie, Val
1778472 Val, Maria, Tanya, David
1828366 Harold
1831061 Alex, David, Ruth
1838853 Eurie, Val
1842616 Eurie, Val
1843444 Alex
1849530 Alex, Stan
1849773 Eurie, Petra
1854158 Karen C
1854546 Alex
1859787 Val
1862141 Colin
1862182 Colin
1862270 Colin
1862997 Colin, Peifen
1863951 Peter
1865813 Jodi
1866061 David, Val
1869710 Karen C, Peter
1873214 Doug
1875064 Peter
1881129 Val


Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1242405 Alex, Tanya
1456948 David, Tanya, Karen C
1835733 David
1837136 David, Peter
1855466 Eurie
1859694 Tanya, David
1864044 David
1864242 David
1865813 Tanya
1866024 Tanya
1866807 David
1867333 David, Tanya
1871191 David, Tanya
1874785 David
1874790 David
1876442 Tanya, David
1876451 David
1876670 Tanya, Chris
1877602 David
1877703 Tanya, Harold, Karen C
1879647 Tanya, David
1881031 Tanya, David


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

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