Jun2010 ontology report

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Ontology Development Report - June 2010

I. Ontology Development


  • Items opened: 76
  • Items closed: 41
  • Items still open: 296
    • assigned: 137
    • unassigned: 159

Completed content items

  • F-P links for all of the transporters/transport [David & Tanya]
  • Pronephros terms for the renal development project [Becky]
  • Various SourceForge items

Content items in progress

  • Lots of preparation for annotation camp [all]
  • Karen attended a meeting "Gene Transcription in Yeast" and got lots of input about the ongoing overhaul of transcription that she is working on with David Hill. They are also working with Karen Eilbeck to improve the alignment of GO and SO in this area (with respect to definitions of DNA sequences involved in transcription, e.g. promoter, transcription factor binding site, etc.). [David & Karen]
  • BP-BP cross products for part_of links, almost finished [David & Tanya]
  • Chemical_terms_in_GO - continuing to edit the GOCHE ontology (chemicals in GO) ready for meeting with CHEBI in July [David, Tanya, Jane & Harold]
  • Cell polarity issues [Val & David]
  • Viral terms - created a branch file ready to merge into main GO [Jane & viral WG]
  • 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)


  • "Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology" undergoing final revisions before publication in Microbiology and Molecular Biology Reviews [Jane, Michelle, PAMGO consortium]
  • Case studies for publication on "revisability" of GO, proposed and coordinated by Sabina Leonelli - in progress (Midori, Jane, Alex, Karen C)

Anything else

  • GOCHE meeting planned late July in CA

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