Jan2009 ontology report
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
- Extensive progress preparing for MF-MF and MF-BP regulates links (Chris, David, Tanya, Jane)
- Publications
- Paper from muscle content meeting revised, and formally accepted (meeting participants, especially Erika, Jen, Giorgio Valle)
- Plan to retire .ontology file format - see Managers_21Jan09
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)