Dec2008 ontology report

Ontology Development & GO Editorial Office Report - December 2008

I. Ontology Development

• SourceForge
  • Items opened: 79
  • Items closed: 74
    • GO Eds: 37
    • MOD curators: 27 (details in Appendix 1)
    • GO Ed/MOD collaborations: 10 (details in Appendix 2)
  • Items still open: 260
    • assigned, GO Eds: 77
    • assigned, MOD curators: 92
    • unassigned: 91

• Content items resolved
  • Several SourceForge items resolved

• Content items in progress
  • Considerable work on cross-products within GO -- see Category:Internal_Cross_Products and Editors_cross-product_implementation_plan (David, Midori, Jane, Jen, Chris)
  • Work on virus-related terms continuing (Jane, Michelle, Candace, Ariane Toussaint, Brenley McIntosh)
  • Continuing work on processes affecting cellular components (Jane, David, Midori, Val, et al.)
  • Signal transduction overhaul continuing; planning content meeting in February or March; latest notes at Signaling_Meeting_Minutes_April_2008_- (Jen, David)
  • Function-process links for electron transport, metabolic pathways (Jen, Harold, et al.; for electron transport see Electron_transport_mf-bp_Sept_2007_onwards.)
  • Quality control reports generated by Chris
    • Regulation (David, Tanya)
    • Multiple part_of parents (several GO curators, especially Tanya & David)
  • Various SourceForge items

• Ontology development report for grant done

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 -- testing task list for 2.0 release available, and most tasks claimed
  • Discussions about handling disjoint relations is OBO-Edit's editor and viewer components
  • Graphviz viewer bug fix; graph editor configuration options (Jen)

• Advocacy/outreach
  • Progress report for grant done
  • Usual gohelp traffic

• Meetings
  • OntoGenesis Meeting Seven: Building an Ontology with Collaborative Protege, EBI, Dec. 15-16 (Jen)
    • Discussions with Protege developer on Protege/OBO-Edit compatibility, loading GO, etc.

• Anything else
  • Developing teaching materials for a Java programming course to be run at the EBI in January (continued; Jen, with EBI programmers and training staff)
  • GO bibliography has 2454 entries

Appendix 1: MOD curators' SF items
1909719 David
1979289 Tanya & David
1988770 Tanya & David
2191580 Tanya & David
2193780 David
2318298 Tanya & David
2339484 Tanya & David
2353161 Tanya & David
2353632 Tanya & David
2356130 David
2356187 Tanya & David
2356404 Tanya & David
2366108 Tanya & David
2371020 Tanya & David
2390981 Donghui
2390994 Donghui
2391052 Doug, David, Tanya
2392308 Tanya & David
2392599 Tanya & David
2392966 David
2393094 Karen C
2393141 Tanya & David
2431412 Tanya & David
2434262 Tanya & David
2444895 Tanya & David
2445344 Tanya & David
2449166 Tanya & David


Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
2208429 Julie, Eurie
2323171 Pascale, Donghui, Eurie
2354293 Tanya & David
2382978 Alex
2393344 Maria, Peter
2406544 Tanya & David
2431695 Karen C, Harold
2435061 Val, Rama
2435063 Val, Rama
2435141 Rama


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

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