Nov2009 ontology report

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Ontology Development & GO Editorial Office Report - November 2009

I. Ontology Development

  • SourceForge
    • Items opened: 115
    • Items closed: 89 (4 duplicates deleted)
    • Items still open: 279
      • assigned: 218
      • unassigned: 61
  • Content items resolved
  • Content items in progress
    • Date set -- January 18, 2010 -- and announced for release of first internal cross-products. Review of sets such as BP-xp-self and CC-xp-self continues; see plan to add internal cross-products. (Jen, Jane, Midori)
    • Work to resume soon on terms for kidney development; content meeting scheduled for January 25, 2010
    • Evaluating new link suggestions and mismatches from ChEBI cross-products; conference call organized (Midori, Chris, Jane, David, ChEBI curators)
    • Continuing to add function-process part-of links in gene_ontology_write.obo and gene_ontology_ext.obo (David, Tanya)
    • Work continues on overhauling terms related to viruses (Jane)
    • Signal transduction overhaul now finishing structure and definitions for top terms, and working on an example signaling pathway; see Signaling_Meeting_Minutes_November_2009 for latest notes (Jen and experts including Sandra Orchard)
    • Quality control continues as usual - reports generated by Chris (cronjobs)
      • Reasoner-based implied links for new regulation terms - also see above (David, Tanya)
      • Multiple part_of parents (several GO curators, especially Tanya & David)
      • Abduced links [[1]](David, Tanya)
      • Problematic regulates terms [[2]](David, Tanya)
    • Various SourceForge items
  • Publications
    • NAR database issue update e-pub available Nov. 17th
    • Molecular Reproduction and Development review e-pub available Nov. 17th
    • Cross-Product paper presented at ICBO published on Nature Precedings, and extended version submitted to JBI
    • CHEBI cross-products used in 2 papers published by Hunter group (see Mike Bada's emails)
    • Manuscript on Taxon triggers in preparation (follow links from main page for recent notes) (Jen)
    • Resuming work on manuscript on regulates relations (Jane, Midori, David, Chris, Tanya, maybe other annotators)

II. GO Editorial Office activities not represented in part I

  • Anything else
    • GO bibliography has 2942 entries

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