July2007 ontology report

Ontology Development & GO Editorial Office Report - July 2007

I. Ontology Development

• SourceForge
  • Items opened: 77
  • Items closed: 72
    • GO Eds: 35
    • MOD curators: 12 (details in Appendix 1)
    • GO Ed/MOD collaborations: 25 (details in Appendix 2)
  • Items still open: 285
    • assigned, GO Eds: 53
    • assigned, MOD curators: 51
    • unassigned: 181

• Cardiovascular physiology: Meeting follow-up work continuing via virtual meetings; file available at go/scratch/gene_ontology_cardio.obo; more detailed information on wiki: http://gocwiki.geneontology.org/index.php/Cardiovascular_physiology/development

• Muscle development: Meeting held in Padova, July 25-26 (http://wiki.geneontology.org/index.php/Muscle_Development). About 80-90 new terms added to gene_ontology_cardio.obo file; post-meeting work in progress. A report will go on the wiki soon.

• GO-CL cross-products: Work has resumed with a webex session held July 26th. Notes on wiki at http://wiki.geneontology.org/index.php/XP:Meetings#2007.2F07.2F26_:_GO-CL_XPs.2C_next_steps; also see http://wiki.geneontology.org/index.php/Logical_Definitions and BBOP Obol wiki.

• Other content items resolved
  • Transporters: High-level changes committed (also see below)
  • Ribosomal RNA processing overhaul committed (http://gocwiki.geneontology.org/index.php/RNA_processing; Harold, Karen C, Ceri)
  • Various small things for SourceForge items

• Other content items in progress
  • Additional incremental progress on sensu terms
  • Transporters: Work on more specific terms, definitions, etc. to resume at end of summer (http://wiki.geneontology.org/index.php?title=Transporters)
  • Various SourceForge items

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
  • Prioritizing additional features for OBO-Edit 2.0

• Software hub group (Jane, Amelia):
  • AmiGO working group (Jane, Amelia)
    • Continuing development to prepare for next AmiGO 1.0 release

• Advocacy group (Jane):
  • Standards for GO tools
  • Slides for general GOC use
  • August newsletter in progress
  • Usual gohelp traffic

• Annotation outreach (Jen) (note: much more detail in Jen's group report)
  • User categories - descriptions
  • Grant proposal in preparation for immunology (Wellcome Trust)

• Conferences/meetings
  • Muscle content meeting (Jen, Erika, Midori; see above)

• Anything else
  • IMG mapping (Jane):
    • IMG functional roles mapping COMPLETE (~2000 terms mapped, ~200 new GO function terms)
    • IMG pathways (500 terms) to commence 6th August
  • metacyc2go update; about 140 new terms (Midori)
  • Search-and-replace script for ontology editing (Jen)
  • GO Bibliography now has 1491 entries

Appendix 1: MOD curators' SF items
1427800 - David, Doug
1745015 - David
1747859 - David
1749719 - David
1751918 - David
1752858 - Doug
1756987 - David
1757574 - David
1757663 - David
1758842 - David
1760941 - Karen C
1761459 - David

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1233407 - Val, transporter wg
1566704 - Chris T
1621572 - Pascale
1660496 - Karen C, Dianna
1707310 - Michelle, Peter
1719897 - Karen C, Val
1723313 - Alex
1727367 - Val
1739177 - Alex
1741102 - Tom Walk (expert)
1746983 - Val, Harold
1747347 - Doug
1747820 - Susan
1748527 - Doug
1752006 - Alex, Susan
1752079 - Val
1752095 - Val
1752111 - Val
1753438 - Val
1753808 - Karen, Rama
1754690 - Val, Rama
1755770 - Pascale
1756236 - Karen C, Val
819299 - Eurie, Val
973913 - Karen C, Val


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

Back to list