May2009 ontology report
Ontology Development & GO Editorial Office Report - May 2009
I. Ontology Development
- SourceForge
- Items opened: 95
- Items closed: 72 (2 duplicates deleted)
- Items still open: 266
- assigned, GO Eds: 82
- assigned, MOD curators: 112
- unassigned: 72
- Content items resolved
- S. pombe GO slim added
- Several SourceForge items resolved
- Content items in progress
- First function-process part-of links have gone live in gene_ontology_write.obo and gene_ontology_ext.obo
- Work on branching organ development (no single wiki page, but relevant to lung, kidney, salivary gland, mammary gland, prostate, and possibly others (David)
- Work continues on overhauling terms related to viruses
- Signal transduction overhaul continuing, as is content meeting planning (Jen and experts including Sandra Orchard)
- 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
- Plans afoot for more work on electron transport (working group, especially expert Rob Gunsalus)
- Work on relationships among multi-organism process regulation terms (Jane, Chris)
- 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
- Manuscript now in (very early, rough stages of) preparation for a paper on introducing the regulates relationships (Midroi & Jane so far; David, Chris and Tanya to join in soon)
- 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
- OBO-Edit working group:
- Porgrammers fixing bugs
- Working group continuing priorities for bug fixes and new features for 2.1
- monthly report available
- Advocacy/outreach (Jane, Jen)
- See monthly report
- Meetings
- London Hopper Colloquium, British Computer Society, London (Jen; poster)
- Publications
- Regulates manuscript (see above; Midori, Jane)
- Anything else
- GO bibliography has 2680 entries