Jan2010 ontology report

Ontology Development Report - January 2010

I. Ontology Development

• SourceForge
  • Items opened: 162
  • Items closed: 150 (7 duplicates and 1 invalid item deleted; 1 item "pending")
  • Items still open: 291
    • assigned: 235
    • unassigned: 56

• Completed content items
  • Regulates cross-products released into gene_ontology_write.obo and gene_ontology_ext.obo
  • Terms added from ASCB - ASCB_2009 (David, Tanya)
  • Various SourceForge items

• Content items in progress
  • Review of internal cross-product sets such as BP-xp-self and CC-xp-self continues; see plan to add internal cross-products. (Jen, Jane, Midori, Chris, David, Tanya)
  • Kidney_Development now under way
    • Successful content meeting held January 25, 2010
    • Follow-up work in progress
  • Further discussion on aligning with ChEBI for cross-products (Midori, Chris, Jane, David, ChEBI curators); also beginning to plan meeting for GO editors to make chemical references in GO internally consistent
  • 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 seeking comments on new draft of structure and definitions for top terms; Webex session scheduled for February 4th; see Signaling_Meeting_Minutes_January_2010 for latest notes (Jen and experts including Sandra Orchard)
  • Extensive work on [taxon triggers]; ontology errors have been corrected; annotation groups have reviewed inconsistencies, and annotations or taxon rules adjusted
  • 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)

• Publications
  • GO cross-product manuscript reviewed; revisions in progress (Chris, David, Jane, Midori, Mike Bada)
  • Case studies for publication on "revisability" of GO, proposed and coordinated by Sabina Leonelli (Midroi, Jane, Alex, Karen C)
  • Continued from November & December:
    • Manuscript on Taxon triggers in preparation, to be submitted to BMC Bioinformatics (Jen, Chris)
    • Resuming work on manuscript on regulates relations (Jane, Midori, David, Chris, Tanya, maybe other annotators)

• Anything else
  • Discussing ways to make ontology editing info (what's been done, when, why, etc.) more readily available to editors, annotators, and users
  • GO bibliography has 3105 entries

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