Aug2009 ontology report

Ontology Development & GO Editorial Office Report - August 2009

I. Ontology Development

• SourceForge
  • Items opened: 81
  • Items closed: 75
  • Items still open: 263
    • assigned: 206
    • unassigned: 57

• Content items resolved
  • New terms from Society for Developmental Biology meeting (see July report)
  • Several SourceForge items resolved

• Content items in progress
  • The plan to add internal cross-products to the go_write (and therefore also go_ext) file is in progress.
  • Work continues on terms for kidney development
  • Evaluating new link suggestions and mismatches from ChEBI cross-products
  • Continuing to add function-process part-of links in gene_ontology_write.obo and gene_ontology_ext.obo
  • Work continues on overhauling terms related to viruses
  • Signal transduction overhaul is going very well; see Signaling_Meeting_Minutes_July_2009#3rd_August_2009 for latest notes (Jen and experts including Sandra Orchard)
  • Also continuing
    • Additional progress on Cellular component organization and biogenesis, in light of internal cross-products
    • Taxon triggers; currently moving "sensu" information from synonyms to definitions (see Taxon-GO_Implementation_April_2009_onwards#5th_August_2009 and Taxon-GO_Implementation_August_28th_2009_onwards for latest)
    • Work on branching organ development (David)
    • Discussion on transcription factor activity and DNA binding; will take to Sept. meeting (email thread)
    • Discussion on cellular component vs. cellular location; will take to Sept. meeting
  • Quality control continues as usual - reports generated by Chris
    • Regulation - also see above (David, Tanya)
    • Multiple part_of parents (several GO curators, especially Tanya & David)
  • Various SourceForge items

• Meetings
  • Organization under way for September GOC and SAB meetings

• Deprecated .ontology file format retired August 1st - see Managers_21Jan09 and GO_Timeline

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

• OBO-Edit working group:
  • Continued testing of OBO-Edit 2.1 beta
  • See meeting minutes from August 4, 13 and [[OEWG_20090825|25], and monthly report
  • ICBO presentations (see above)

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

• Anything else
  • GO bibliography has 2829 entries

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