May2007 ontology report

Ontology Development & GO Editorial Office Report - May 2007

I. Ontology Development

• SourceForge
  • Items opened: 91
  • Items closed: 71
    • GO Eds: 38
    • MOD curators: 20 (details in Appendix 1)
    • GO Ed/MOD collaborations: 13 (details in Appendix 2)
  • Items still open: 280
    • assigned, GO Eds: 48
    • assigned, MOD curators: 49
    • unassigned: 183

• Collaboration with the Harvard/MIT GO Engineering group: A new draft of a manuscript describing the work has been circulating, and will be submitted to Nature Genetics as a Perspectives piece.

• Cardiovascular physiology: file gene_ontology_cardio.obo contains about 50 new terms; organization based on physiology; links to SIMAP to be added. Meeting planned for June. Wiki: http://gocwiki.geneontology.org/index.php/Cardiovascular_physiology/development

• Other content items resolved
  • Various small things for SourceForge items

• Other content items in progress
  • Ribosomal RNA processing overhaul nearly complete (Harold, Karen C, Ceri)
  • A small amount of progress on the sensu and taxon items
  • Transporters (http://wiki.geneontology.org/index.php?title=Transporters)
  • Muscle development: Meeting planned for last week July (exact dates TBD soon); preparatory editing coordinated by Erika and Jen (http://wiki.geneontology.org/index.php/Muscle_Development).
  • Suggestions on cell cycle-related terms from expert in Ghent (via Jane)
  • Resolving disjointness violations in the process ontology (Jane and David; almost finished)

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

• OBO-Edit working group:
  • OBO-Edit 2.0 first beta released
  • Bioinformatics Application Note in final throes of publication logistics (actually published as of June 1st)
  • Paper on graphical editing in OBO-Edit 2.0 submitted to Bio-ontologies SIG at ISMB

• Software hub group (Jane, Amelia):
  • AmiGO working group (Jane, Amelia)
    • Continuing development to prepare for June AmiGO (1.0) release
  • Prototype of SourceForge tracker submission tool being tested (programmed by Seth; tested by AWG and GO Eds)

• Advocacy group (Jane):
  • May newsletter released
  • Some GO web site maintenance (Amelia)
  • Usual gohelp traffic (slightly busier than last couple months)

• Annotation outreach (Jen) (note: much more detail in Jen's group report)
  • SOP discussions continuing
    • New SOP web page available (help from Amelia), with ISS flowchart
    • Flowcharts in preparation for IEA and for top-level annotation decisions

• Conferences/meetings
  • Agro-genomics workshop on plant annotation, Ghent: GO talk and OBO-Edit demo (Jane)
  • Planning for cardio content meeting (David, Simon, experts; see above)
  • Planning for muscle content meeting (Jen, Erika; see above)

• Anything else
  • IMG mapping in progress (Jane)
  • GO Bibliography now has 1392 entries

Appendix 1: MOD curators' SF items
856170 - Karen C, Val
1585409 - Karen C, Tanya
1706567 - David
1708418 - Donghui, Karen C
1708446 - Donghui, Karen C
1708896 - Donghui
1710878 - Donghui
1711493 - Donghui
1711867 - David
1718700 - David
1720004 - David
1721422 - David
1722202 - David
1722719 - David
1722869 - David
1723513 - David
1723697 - David
1723705 - David
1725863 - Alex, Petra, Harold
1727948 - Donghui

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1469444 - Alex
1491013 - Chandra, Val, Michelle
1633338 - Harold
1657892 - Karen C
1702938 - Val, community expert
1705071 - Val
1707593 - Tanya, community expert
1708213 - Karen C, Val
1710159 - Cathy Derow (IntAct)
1710724 - Eurie, Val
1714238 - Kirill
1715584 - Ranjana
1717390 - Doug

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

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