June2007 ontology report

Ontology Development & GO Editorial Office Report - June 2007

I. Ontology Development

• SourceForge
  • Items opened: 62
  • Items closed: 62
    • GO Eds: 42
    • MOD curators: 5 (details in Appendix 1)
    • GO Ed/MOD collaborations: 15 (details in Appendix 2)
  • Items still open: 279
    • assigned, GO Eds: 57
    • assigned, MOD curators: 49
    • unassigned: 173

• Cardiovascular physiology: 1.5 day meeting held at Medical College of Wisconsin; about 100 new terms added, mainly on renal control of blood pressure. Work continues via virtual meetings; file available at go/scratch/gene_ontology_cardio.obo; more detailed description of meeting on wiki: http://gocwiki.geneontology.org/index.php/Cardiovascular_physiology/development

• Other content items resolved
  • Disjointness violations in process ontology resolved (Jane and David)
  • Some additions/updates for PAMGO (Jane)
  • All cellular component terms now defined
  • Various small things for SourceForge items

• Other content items in progress
  • Ribosomal RNA processing overhaul nearly complete (Harold, Karen C, Ceri)
  • Additional incremental progress on sensu terms
  • Transporters: draft sent to GO list for comment; will be implemented 1st week July (http://wiki.geneontology.org/index.php?title=Transporters)
  • Muscle development: Meeting planned for July 25-26 (http://wiki.geneontology.org/index.php/Muscle_Development).
  • More work on cell cycle-related suggestions (Midori, Val, Eurie, Rob)

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

• OBO-Edit working group:
  • Additional OBO-Edit 2.0 betas released; demos and testing under way

• Software hub group (Jane, Amelia):
  • AmiGO working group (Jane, Amelia)
    • Continuing development to prepare for next AmiGO 1.0 release
    • Discussing various interface options
  • Further work on SourceForge tracker submission tool (programmed by Seth; tested by AWG and GO Eds)

• Advocacy group (Jane):
  • Usual gohelp traffic; a few more curators have joined the rota

• Annotation outreach (Jen) (note: much more detail in Jen's group report)
  • More work on flowcharts
  • Jen has learned the art of UniProt GO annotation from Emily

• Conferences/meetings
  • Wellcome Advanced Course: Functional Genomics - talk on "Using GO for analysis of expression data" (Jane)
  • Cardio content meeting (David, Simon, experts; see above)
  • Planning for muscle content meeting (Jen, Erika; see above)
  • Fact-finding on running annotation/ontology development courses at EBI (Jen, for Ruth Lovering & WT grant application)

• Anything else
  • IMG mapping: "terms" done; "pathways" in progress (Jane)
  • GO Bibliography now has 1451 entries

Appendix 1: MOD curators' SF items
1723713 - David
1728531 - David
1723691 - David, Maria, Val
1730751 - David
1732046 - David

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1578969 - Eurie, Val
1731073 Chris, Melissa
1729186 - Petra
1731477 - Karen C
1734036 - Karen C
1499218 - Sue, Donghui
1741185 - Michelle
1741376 - Matt, David Roos (community expert)
1740879 - David, Louise Dougherty
1742917 - Alex
1728308 - Vladimir Mironov (community expert)
1728275 - Val
1744717 - Val
1728276 - Val
1728279 - Val, Rob, Eurie


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

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