Jun2009 ontology report

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Ontology Development & GO Editorial Office Report - June 2009

I. Ontology Development

  • SourceForge
    • Items opened: 91
    • Items closed: 112 (3 duplicates and one other deleted)
    • Items still open: 242
      • assigned, GO Eds: 85
      • assigned, MOD curators: 103
      • unassigned: 54
  • Content items resolved
    • Several SourceForge items resolved
  • Content items in progress
    • Cross-products - see notes above
    • Has_part relationship - see notes above
    • Continuing to add function-process part-of links in gene_ontology_write.obo and gene_ontology_ext.obo
    • Work continues on overhauling terms related to viruses; mailing list created
    • Signal transduction overhaul continuing; content meeting date set (Jen and experts including Sandra Orchard)
    • Also continuing
      • Additional progress on Cellular component organization and biogenesis, in light of internal cross-products
      • Taxon triggers - workflow improved; implementation in progress
      • Work on branching organ development (David)
      • Electron transport (working group)
      • 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 in preparation for paper on the regulates relationships on hold due to vacations, meetings, etc. (Midori & Jane so far; David, Chris and Tanya to join in soon)
  • Meetings
    • Jane gave talk for OBO Foundry meeting (June)
      • (Other GO people also attended; they can fill in anything they see fit here.)
    • David planning for Society for Developmental Biology meeting (July; poster)

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

  • Advocacy/outreach (Jane, Jen)
    • EBI outreach team planning plant bioinformatics course; Jen contributing GO coverage
    • See monthly report
  • Meetings
    • OBO Foundry meeting June 7-8 (Jane)
    • Chris' visit to EBI office (see above)
  • Publications
    • PAMGO paper "Applying the Gene Ontology in Microbial Annotation" accepted by Trends in Microbiology for publication in July (PAMGO group, plus Jane)
  • Anything else
    • GO bibliography has 2728 entries

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