Jan2009 ontology report

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Ontology Development & GO Editorial Office Report - January 2009

I. Ontology Development

  • SourceForge
    • Items opened: 104
    • Items closed: 93 (5 duplicates deleted)
      • GO Eds: 42
      • MOD 25 (details in Appendix 1)
      • GO Ed/MOD collaborations: 26 (details in Appendix 2)
    • Items still open: 267
      • assigned, GO Eds: 85
      • assigned, MOD curators: 110
      • unassigned: 72
  • Content items resolved
    • More PAMGO terms (Jane)
    • Several SourceForge items resolved
  • Content items in progress
    • Extensive progress preparing for MF-MF and MF-BP regulates links (Chris, David, Tanya, Jane)
      • Consistency checks, e.g. ensuring that there's a corresponding MF term for every regulation-of-some-function BP term
      • See FP-regulates and GO_Timeline; additional wiki notes forthcoming
      • Multi-organism process MF-BP regulates links (Jane)
      • Additional proposal on function terms defined by process forthcoming; for now see Managers_21Jan09
    • Additional work on cross-products within GO -- see Category:Internal_Cross_Products and Editors_cross-product_implementation_plan (David, Midori, Jane, Jen, Chris, Tanya)
    • Signal transduction overhaul continuing, as is content meeting planning; latest notes at Signaling_Meeting_Minutes_April_2008_- (Jen, David)
    • Planning small content meeting for prokaryotic electron transport (Rob Gunsalus, working with Jen and rest of electron transport WG)
    • Quality control reports generated by Chris (ongoing work)
      • Regulation - also see above (David, Tanya)
      • Multiple part_of parents (several GO curators, especially Tanya & David)
    • Various SourceForge items
  • Publications
    • Paper from muscle content meeting revised, and formally accepted (meeting participants, especially Erika, Jen, Giorgio Valle)

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 -- considerable progress working through testing task list for 2.0 release
    • Graph editor help guide revised and extended (Jen)
    • Graphviz viewer and graph editor bug fixes (Jen)
  • Advocacy/outreach
    • Drupal news feed set up
    • Usual gohelp traffic
  • Meetings
    • OntoGenesis meeting on collaborative ontology development using the Cell Ontology (Midori)
    • Biocurator meeting abstracts submitted
    • Content meeting planning (see above)
  • Publications
    • Muscle paper (see above)
  • Anything else
    • GO links for PathEpigen mapping (Jane)
    • Organized & presented beginner-level Java programming course held at the EBI (Jen, with EBI programmers and training staff)
    • GO bibliography has 2496 entries
Appendix 1: MOD curators' SF items
1757927 Alex
1982415 Donghui
2082712 Donghui, Kate
2403273 Tanya, David
2433996 Donghui
2443283 Donghui
2443315 Donghui
2443361 Donghui
2443389 Donghui
2443620 Donghui
2445843 Donghui
2492935 Tanya
2494023 Tanya, David, Jim
2503103 Rama
2504053 Tanya, David, Val
2504280 Tanya, David
2505145 Tanya, David
2509709 David
2510100 Tanya, David
2513277 Tanya, David
2514240 Tanya, David
2523989 David
2531248 Tanya, David
2537560 Tanya, David
2543060 Tanya, David


Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1745083 Alex, Candace, Petra
1747887 Colin, David
1762858 Chris, David
1811601 Maria, Val
1860356 Eurie
1940353 Karen C
2019739 Tanya, David
2415872 Alex (also some obi-biomaterial group members)
2445911 Donghui
2488463 Harold
2494121 Alex, Candace, Petra
2494467 Alex
2505783 Eurie
2506514 Maria
2507143 Eurie
2507167 Eurie
2507195 Eurie
2507196 Tanya
2507331 Eurie, Rama, Val
2507373 Rama
2512097 Karen C, Julie
2520134 Maria, Val
2528716 Michelle, Val
2531491 Stan
2531818 Donghui
2545760 PAMGO curators


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

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