Apr2009 ontology report

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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
  • Metrics now organized in wiki category

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
  • 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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