Sep2009 ontology report

Ontology Development & GO Editorial Office Report - August 2009

I. Ontology Development

• SourceForge
  • Items opened: 110
  • Items closed: 102
  • Items still open: 271
    • assigned: 209
    • unassigned: 62

• Content items resolved
  • Improvements to RNA interference and related terms
  • Several SourceForge items resolved, including some handled at GO meeting "clinic" session

• Content items in progress
  • Additions from heart development content meeting held at UCL September 22, 2009 (David, Varsha, Doug, et al.)
  • 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; finished moving "sensu" information from synonyms to definitions. Now resolving the inconsistencies found using the rules and Chris's script (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)
  • Quality control continues as usual - reports generated by Chris
    • 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 (David, Tanya)
    • Problematic regulates terms (David, Tanya)
  • Various SourceForge items

• Meetings
  • Heart development content meeting (see above)
  • Cambridge Combined GO Consortium and SAB Meeting Jesus College, Cambridge, UK, September 23-25, 2009 - also see GOC Meeting Minutes September 2009

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 September 3, 15 and 24, and monthly report

• Advocacy/outreach (Jane, Jen)
  • Cambridge Clinical Neuroscience and Mental Health Symposium, 29th - 30th September 2009 (Jen - poster)
  • See monthly report

• Anything else
  • GO bibliography has 2829 entries

Back to list