Mar2009 ontology report

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Ontology Development & GO Editorial Office Report - March 2009

I. Ontology Development

  • SourceForge
    • Items opened: 108
    • Items closed: 94
      • Note: Due to changes in SourceForge's tracker system, the breakdown of SF items resolved by MOD curators, GO editorial office curators, and MOD-GOed collaborations cannot easily be determined for March 2009. Midori has submitted a feature request to have the relevant feature (ability to sort closed items by close date) restored, but there has been no response so far. From April onwards, a workaround would be possible but would take a lot more time.
    • Items still open: 272
      • assigned, GO Eds: 85
      • assigned, MOD curators: 127
      • unassigned: 60

The main thing for March, of course, has been preparation for and participation in the GO Consortium meeting in Eugene, Oregon. A progress report prepared for the meeting is available.

  • Presented at meeting:
  • Content items resolved
    • Several 'activator' and 'inhibitor' terms obsolete for consistency with obsolete function terms
    • Several SourceForge items resolved
  • Content items in progress (much the same as last month)
    • 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 (Jen, David, experts)
    • Planning continues for small content meeting for prokaryotic electron transport (Rob Gunsalus, working with Jen and rest of electron transport WG)
    • Cellular component organization and biogenesis almost done
    • 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
    • Agreed to contribute a chapter on ontology development approaches used in GO, for book entitled Knowledge-Based Bioinformatics: From Analysis to Interpretation, edited by Marco Ramoni and Gil Alterovitz (our GO Engineering collaborators) (David, Tanya, Chris, Judy, maybe others as needed)

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 release candidate now being tested, bugs fixed, etc. Release planned for April 7, 2009.
    • Colin Batchelor has joined working group
    • monthly report available
  • Meetings
    • GOC meeting (see above)
    • Biocurator meeting preparation
    • "Clackpoint" VOIP software trial (OBO-Edit working group meeting)
  • Anything else
    • GO bibliography has 2575 entries
Appendix 1: MOD curators' SF items
NOT AVAILABLE FOR MARCH 2009

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
NOT AVAILABLE FOR MARCH 2009

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

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