Feb2009 ontology report

Ontology Development & GO Editorial Office Report - February 2009

I. Ontology Development

• SourceForge
  • Items opened:
  • Items closed:
    • GO Eds:
    • MOD (details in Appendix 1)
    • GO Ed/MOD collaborations: (details in Appendix 2)
  • Items still open:
    • assigned, GO Eds:
    • assigned, MOD curators:
    • unassigned:

• Content items resolved
  • MF-MF and MF-BP regulates links live in gene_ontology_ext.obo (Chris, David, Tanya, Jane)
    • For more information, see the January ontology development report and the January 21st managers' call minutes
  • More PAMGO terms (Jane)
  • Several SourceForge items resolved

• Content items in progress
  • Additional work on cross-products within GO -- see Category:Internal_Cross_Products and Editors_cross-product_implementation_plan (David, Midori, Jane, Jen, Chris, Tanya)
  • Signal transduction overhaul continuing, as is content meeting planning; latest notes at Signaling_Meeting_Minutes_April_2008_- (Jen, David)
  • Planning continues for small content meeting for prokaryotic electron transport (Rob Gunsalus, working with Jen and rest of electron transport WG)
  • Quality control reports generated by Chris (ongoing work)
    • Regulation - also see above (David, Tanya)
    • Multiple part_of parents (several GO curators, especially Tanya & David)
  • Various SourceForge items

• Publications
  • Paper from muscle content meeting published (meeting participants, especially Erika, Jen, Giorgio Valle)

PubMed abstract full text

• Ontology publishing pipeline revised
  • New checks to be put in place -- see go/software/utilities/check-obo-for-standard.release.pl

• Reminder: plan to retire .ontology file format - see Managers_21Jan09

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

• Amelia at Berkeley

• OBO-Edit working group:
  • OBO-Edit 2 testing -- considerable progress working through testing task list for 2.0 release; plans for final testing and WG sign-off in mid-March
  • Also see report

• Advocacy/outreach
  • Meeting with Mauno Vihinen to discuss his plan for a mutation ontology. Introduced him to Karen Eilbeck to follow up. (Jen)
  • Also see report
  • Usual gohelp traffic

• Meetings
  • Content meeting planning (see above)

• Publications
  • Muscle paper (see above)

• Anything else
  • GO bibliography has 2544 entries

Appendix 1: MOD curators' SF items


Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved


(Note: "MOD curator" is shorthand for any non-GO-Ed curator)

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