Mar2008 ontology report: Difference between revisions
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Latest revision as of 07:08, 2 April 2009
Ontology Development & GO Editorial Office Report - March 2008
I. Ontology Development
- SourceForge
- Items opened: 56
- Items closed: 48
- GO Eds: 32
- MOD curators: 4 (details in Appendix 1)
- GO Ed/MOD collaborations: 12 (details in Appendix 2)
- Items still open: 281
- assigned, GO Eds: 56
- assigned, MOD curators: 63
- unassigned: 162
- Content items resolved
- 'Regulates' relationships live (yay!) (David, Tanya, Chris, et al.)
- Electron transport reorganization live (Jen and electron transport wg)
- Sporulation terms reorganized (connected with the last of the sensu revamp, http://wiki.geneontology.org/index.php/Sporulation_Meeting_Notes)
- Several SourceForge items resolved
- Content items in progress
- Follow-up to 'regulates' work -- David and Tanya are still correcting errors reported by Chris' QC scripts; error reports will continue to be generated at least until OBO-Edit 2.0 is released (http://wiki.geneontology.org/index.php/Regulation_Main_Page).
- Function-process pilot projects under way (http://wiki.geneontology.org/index.php/Function-Process_Links)
- electron transport
- glycolysis & TCA cycle (Harold)
- Lipoprotein-related process and component terms - small collaboration with UCL and Reactome (Midori)
- Signal transduction overhaul (Jen doing initial work and finding experts)
- Additional transport work (Jen plus experts including Steve Oliver's group)
- Initial exploration of plant processes affected by herbicides
- Various SourceForge items
- IMG mapping update in progress (Jane)
- Switched to new go/ontology/directory structure ( Ontology_CVS_Directory_Layout_Overhaul )
See monthly report in CVS for ontology statistics.
II. GO Editorial Office activities not represented in part I
- Jane's back!
- Amelia is preparing for another stint at Berkeley
- OBO-Edit working group:
- More bug testing and documentation for OBO-Edit 2.0 (it never ends ...)
- Jen contributing to programming (e.g. GUI for obomerge)
- Advocacy/outreach
- AmiGO release to use 'regulates'
- GO demo for WTGC master's students
- Discussion with Steve Oliver on Aspergillus annotation jamboree
- Meetings
- GO talk and AmiGO demo at EBI training roadshow, Ghent (Jen)
- Workshop on "Making Small Facts Travel: Labels, Packages and Vehicles", London School of Economics (Midori)
- Anything else
- Chapter featuring GO and new AmiGO in "Bioinformatics for Tropical Disease Research: A Practical and Case-Study Approach" (Jane and Matt Berriman; http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=bioinfo.TOC&depth=2)
- GO bibliography has 1876 entries
Appendix 1: MOD curators' SF items 1863992 David, Tanya 1912005 David 1929541 David 1929546 David, Tanya Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved 1192485 Harold, Val 1807790 Jim 1881722 sporulation group 1894620 Peter 1898404 Chris, Alex, David 1901792 Karen C 1908887 Cindy 1909714 Rama 1911038 Alex 1911964 Rama, Val 1916944 Julie 1929533 Alex (Note: "MOD curator" is shorthand for any non-GO-Ed curator)