May2009 ontology report

Ontology Development & GO Editorial Office Report - May 2009

I. Ontology Development

• SourceForge
  • Items opened: 95
  • Items closed: 72 (2 duplicates deleted)
  • Items still open: 266
    • assigned, GO Eds: 82
    • assigned, MOD curators: 112
    • unassigned: 72

• Content items resolved
  • S. pombe GO slim added
  • Several SourceForge items resolved

• Content items in progress
  • First function-process part-of links have gone live in gene_ontology_write.obo and gene_ontology_ext.obo
  • Work on branching organ development (no single wiki page, but relevant to lung, kidney, salivary gland, mammary gland, prostate, and possibly others (David)
  • Work continues on overhauling terms related to viruses
  • Signal transduction overhaul continuing, as is content meeting planning (Jen and experts including Sandra Orchard)
  • Additional progress on Cellular component organization and biogenesis (just a few bits remaining now)
  • Taxon triggers - some progress, limited by OBO-Edit filtered-save options
  • Plans afoot for more work on electron transport (working group, especially expert Rob Gunsalus)
  • Work on relationships among multi-organism process regulation terms (Jane, Chris)
  • 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

• Manuscript now in (very early, rough stages of) preparation for a paper on introducing the regulates relationships (Midori & Jane so far; David, Chris and Tanya to join in soon)

• Meetings
  • Jane preparing talk for OBO Foundry meeting (June)
  • David planning for Society for Developmental Biology meeting (July; poster)

• Chris has made progress on inference that can be done on a gene-association file (this will be in the software report, and is mainly an annotation issue, but we're mentioning it here to give it that bit more coverage).

• Reminder: plan to retire .ontology file format - 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:
  • Porgrammers fixing bugs
  • Working group continuing priorities for bug fixes and new features for 2.1
  • monthly report available

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

• Meetings
  • London Hopper Colloquium, British Computer Society, London (Jen; poster)

• Publications
  • Regulates manuscript (see above; Midori, Jane)

• Anything else
  • GO bibliography has 2680 entries

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