Feb2009 ontology report
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Ontology Development & GO Editorial Office Report - February 2009
I. Ontology Development
- SourceForge
- Items opened: 84
- Items closed: 91
- GO Eds: 50
- MOD 11 (details in Appendix 1)
- GO Ed/MOD collaborations: 50 (details in Appendix 2)
- Items still open: 258
- assigned, GO Eds: 86
- assigned, MOD curators: 115
- unassigned: 57
- Content items resolved
- MF-MF and MF-BP regulates links live in gene_ontology_ext.obo (Chris, David, Tanya, Jane)
- For more information, see the January ontology development report and the January 21st managers' call minutes
- More PAMGO terms (Jane)
- Several SourceForge items resolved
- MF-MF and MF-BP regulates links live in gene_ontology_ext.obo (Chris, David, Tanya, Jane)
- Content items in progress
- 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 continues for 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 published (meeting participants, especially Erika, Jen, Giorgio Valle)
- Ontology publishing pipeline revised
- New checks to be put in place -- see go/software/utilities/check-obo-for-standard.release.pl
- Reminder: 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; plans for final testing and WG sign-off in mid-March
- Also see report
- Advocacy/outreach
- Meeting with Mauno Vihinen to discuss his plan for a mutation ontology. Introduced him to Karen Eilbeck to follow up. (Jen)
- Also see report
- Usual gohelp traffic
- Meetings
- Content meeting planning (see above)
- Publications
- Muscle paper (see above)
- Anything else
- GO bibliography has 2544 entries
Appendix 1: MOD curators' SF items 2513373 David, Tanya 2523951 David, Tanya 2531604 David, Tanya 2545211 David, Tanya 2565393 Tanya 2568753 David, Tanya 2569392 Tanya 2569613 Tanya 2573254 Tanya 2589176 Tanya 2617157 Harold Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved 1806214 Colin 1853360 Val, David 1866852 Colin 1993246 Erika, Paolo Laveder (community expert) 2012346 Julie, Rama 2018086 Julie 2067787 Karen C, Val 2374080 David, Tanya 2391140 Kate 2510017 David 2526210 David, Tanya 2528641 electron transport wg 2528656 Tanya 2550022 Karen C 2560505 transport wg 2573002 Val 2586582 Kate 2590374 John Garavelli 2593252 Maria 2593300 Maria 2593745 Harold 2593932 Alex 2597089 Julie, Rama 2597296 Alex 2597333 Alex 2606668 Harold 2611474 Alex 2625065 Alex 2631894 Doug 2632430 Kate 2637136 Tanya (Note: "MOD curator" is shorthand for any non-GO-Ed curator)