Dec2009 ontology report

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Ontology Development & GO Editorial Office Report - December 2009

I. Ontology Development

  • SourceForge
    • Items opened: 100
    • Items closed: 90 (2 duplicates deleted)
    • Items still open: 287
      • assigned: 213
      • unassigned: 74
  • Content items in progress
    • Terms added from ASCB - about 150 so far, with more to come; COPII vesicle-mediated transport, cholesterol transport, cell migration, sphingolipid metabolism, organelle fission/fusion, eye morphogenesis (David, Tanya)
    • Release of first internal cross-products on track for January 18, 2010. Review of sets such as BP-xp-self and CC-xp-self continues; see plan to add internal cross-products. (Jen, Jane, Midori, Chris, David, Tanya)
    • Work to resume soon on terms for kidney development; content meeting scheduled for January 25, 2010
    • Conference call held on evaluating new link suggestions and mismatches from ChEBI cross-products (Midori, Chris, Jane, David, ChEBI curators); minutes available in ontology-editors list archive
    • 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: new draft of structure and definitions for top terms, and an example signaling pathway, now completed and soon to be available for comment; see Signaling_Meeting_Minutes_December_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
    • Manuscript on taxon triggers in preparation, to be submitted to BMC Bioinformatics (Jen, Chris)
    • Continued from November:
      • 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 3034 entries

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