Jul2010 ontology report

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Ontology Development Report - July 2010

I. Ontology Development

Tracker

  • Items opened: 100
  • Items closed: 62
  • Items still open: 311
    • assigned: 157
    • unassigned: 154

Completed content items

  • Updated GO to match the latest MetaCyc mappings [Amelia]
  • A new set of interaction between organism terms added for PAMGO, including several cc terms [Jane]
  • Various SourceForge items [all]

Content items in progress

  • Overhaul of transcription proposal complete, and has been sent out to GOC for comments. Almost ready to proceed with edits [David & Karen]
  • Final stages of checking the BP-BP cross-products. Clean-up done (all 'during' terms fixed), now need to look at the reasoner results and fix up the details [David & Tanya]
  • Chemicals in GO project: we had a successful GOCHE meeting, with CHEBI, 22-25 July. Next steps are to add missing GOCHE terms to CHEBI, make some fixes to GO and CHEBI then make CHEBI xps in GO. [David, Tanya, Jane & Harold]
  • Ready to commit mesonephros terms for kidney project [David]
  • Automatic cross product term submission tool almost ready to release to wider group (regulates terms only) [Chris, Seth, Jane, David, Tanya, Amelia]
  • F-P links for transporters complete. Beginning work on catalytic activity [David, Tanya]
  • Quality control continues as usual - reports generated by Chris (cronjobs)
    • Reasoner-based implied links for new regulation terms - also see above (David, Tanya)
    • Abduced links [[1]](David, Tanya)

Publications

  • Heart development paper is in the draft stage [David, Varsha]
  • GOCHE paper manuscript started [David, Tanya, Jane & Harold]
  • "Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology" accepted by 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

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