Apr2009 ontology report
Ontology Development & GO Editorial Office Report - March 2009
I. Ontology Development
- SourceForge
- Items opened: 129
- Items closed: 153 (3 duplicates deleted)
- Items still open: 245
- assigned, GO Eds: 81
- assigned, MOD curators: 106
- unassigned: 58
The biggest single news item for April is that OBO-Edit 2.0 has been released, and is now used for editing GO and to generate files derived from gene_ontology_write.obo (see GO_Timeline for details).
- Content items resolved
- Several SourceForge items resolved
- Content items in progress (much the same as last month)
- Specific planning for 1:1 function-process part-of links
- Work is under way on overhauling terms related to viruses
- Signal transduction overhaul continuing, as is content meeting planning (Jen and experts including Sandra Orchard)
- new high-level structure in place in draft file; more specific terms being placed
- Additional work on cross-products within GO -- see Category:Internal_Cross_Products and Editors_cross-product_implementation_plan (David, Midori, Jane, Jen, Chris, Tanya)
- Additional progress on Cellular component organization and biogenesis (just a few bits remaining now)
- Taxon triggers - some progress, limited by OBO-Edit filtered-save options
- Work on relationships among multi-organism process regulation terms (Jane, Chris)
- A working group has been formed to discuss the usage of binding MF terms. It's mainly focused on annotation, but may have some effect on ontology content.
- Quality control continues as usual - reports generated by Chris
- Regulation - also see above (David, Tanya)
- Multiple part_of parents (several GO curators, especially Tanya & David)
- Various SourceForge items
- Meetings
- Several ontology developers attended the Third International Biocurator Conference, April 16-19, Berlin (see http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html)
- Poster for London Hopper Colloquium next month (Jen)
- Metrics now organized in wiki category
- Reminder: plan to retire .ontology file format - see Managers_21Jan09 and GO_Timeline
See monthly report in CVS for ontology statistics.
II. GO Editorial Office activities not represented in part I
- Erika Feltrin (Padua) back from maternity leave
- OBO-Edit working group:
- OBO-Edit 2 released!
- Working group now setting priorities for bug fixes and new features for 2.1
- Thomas Waechter has updated the Ontology Generation plugin
- monthly report available
- Advocacy/outreach
- Highlight: News feed has gone live at http://go.berkeleybop.org/news4go/
- See monthly report for more
- Meetings
- Biocurator meeting (see above; Midori, Jane, Jen)
- Publications
- Aspergillus nidulans genome annotation PMID:19146970 (Jen among many authors)
- OBO naming conventions PMID:19397794 (Jane & Chris among authors)
- Anything else
- GO bibliography has 2617 entries