Apr2009 ontology report

Ontology Development & GO Editorial Office Report - April 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

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