Jan2010 ontology report

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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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