May2009 ontology report

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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 (Midori & Jane so far; David, Chris and Tanya to join in soon)
  • Meetings
    • Jane preparing talk for OBO Foundry meeting (June)
    • 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

  • OBO-Edit working group:
    • Programmers fixing bugs
    • Working group continuing priorities for bug fixes and new features for 2.1
    • monthly report available
  • Meetings
    • London Hopper Colloquium, British Computer Society, London (Jen; poster)
  • Publications
    • Regulates manuscript (see above; Midori, Jane)
  • Anything else
    • GO bibliography has 2680 entries

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