Nov2009 ontology report

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
  • Additions and modifications made during and after the heart development content meeting held at UCL September 22, 2009 (David, Varsha, Doug, et al.)

• 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

• OBO-Edit working group:
  • See meeting minutes from November 3, 17 and 24, and monthly report

• Advocacy/outreach (Jane, Jen)
  • See monthly report

• Anything else
  • GO bibliography has 2942 entries

Back to list