Feb2007 ontology report

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Ontology Development & GO Editorial Office Report - February 2007

I. Ontology Development

  • SourceForge
    • Items opened: 84
    • Items closed: 94
      • GO Eds: 30
      • MOD curators: 23 (details in Appendix 1)
      • GO Ed/MOD collaborations: 41 (details in Appendix 2)
    • Items still open: 277
      • assigned, GO Eds: 50
      • assigned, MOD curators: 79
      • unassigned: 198
  • Work on the 'sensu' terms is well under way; changes are being made "live," i.e. in gene_ontology_edit.obo rather than in a separate ontology file. Detailed progress reports are available on the wiki (go to the Sensu main page and follow the 'Meeting Notes' link).
  • Planning & preparation continue for the meeting on the collaboration with Jonathan Liu et al. at MIT.
  • Plans are firming up for ceating links between function and process terms. We'll start with metabolic pathways, and have our biochemically inclined curators start identifying links (using available resources such as Reactome) in parallel with Chris and Amelia sorting out the actual relationship to be used. More details available on the wiki and in manager conf call notes.
  • Other content items in progress
    • Resolving disjointness violations in the process ontology (Jane, using file of violations identified by Chris)
    • Protein modification (Jane, John Garavelli)
    • Regulation of process terms - check for consistency with process terms (David, using file from Chris)

David & Midori have looked over the outstanding SourceForge items, and are ready to start assigning many of them to GO curators (both GO Eds and MOD curators) based on biological areas of expertise.

We have implemented the first part of our nascent system for crediting community experts who contribute to ontology development: one abstract has been added to the GO_REFs file (CCNS meeting), another is in the works (immunology), and a syntax has been established for citing them. Additional info is in manager call minutes and on the GO list.

See monthly report in CVS for ontology statistics.


II. GO Editorial Office activities not represented in part I

  • OBO-Edit working group:
    • OBO-Edit 1.1 beta testing continues; a few more bugs have been fixed.
    • A (slightly) revised manuscript for the applications note has been submitted to Bioinformatics, along with a response to reviewers' comments.
  • Software hub group (Jane, Amelia):
    • AmiGO working group (Jane, Amelia)
      • AmiGO now running on faster servers, and from new URL, http://amigo.geneontology.org
      • Setting priorities for feature additions
      • Interface and search enhancements in progress
      • Testing ongoing (features, interface, bug fixes, etc)
  • Advocacy group (Jane):
    • February newsletter is out
    • Tool requirments document in preparation
    • Meetings calendar on internal wiki
    • Usual gohelp traffic
  • Annotation outreach (Jen) (note: much more detail in Jen's group report)
    • Flowcharts for annotation procedures in preparation
    • Metrics likewise
  • Conferences/meetings
    • GO-MIT (see aboeve)
    • Planning for muscle content meeting (Jen, Erika)
    • Signaling meeting at Sanger - Jen attended
  • Anything else
    • GO Bibliography now has 1281 entries
    • Jen has helped Erika get software set up
Appendix 1: MOD curators' SF items

1604888 - Donghui, Tanya
1644804 - Donghui
1644819 - Donghui
1644838 - Donghui
1644868 - Donghui
1646949 - David
1649857 - David
1650780 - Becky
1653574 - Donghui
1653971 - David, Becky
1654525 - Harold, Rama
1659249 - David
1659952 - Donghui
1660958 - Donghui
1661017 - Donghui, Tanya
1661597 - David
1661624 - David
1661722 - David
1664533 - Harold
1665537 - David
1666457 - David

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1378881 - David, Karen P, Pascale
1400564 - Chris T
1431082 - Melissa
1432177 - Nick Thomson
1516347 - Martha Arnaud
1526200 - Karen C
1562205 - Many, including David, Tanya, Michelle
1636063 - Several, including Evelyn, Emily, Val, Karen C
1643043 - Julie
1645488 - John Garavelli
1646580 - Rama
1646614 - Rama, Val
1647142 - Alex
1647347 - David, Tanya
1647477 - Rama, Kimberly
1647990 - Maria
1648258 - Rama, Michelle
1649153 - Michelle
1649617 - David
1650586 - PAMGO curators
1650742 - Maria, Rama
1650749 - Alex, Karen C
1652331 - Rama
1652350 - Rama
1652475 - Jodi
1653399 - Harold
1653490 - Rama, Becky, Val
1653493 - Rama
1653518 - Rama, Becky
1653565 - Donghui
1654108 - Rama, Val
1654151 - Becky
1655351 - David, Melissa
1656404 - Karen C
1658303 - Alex
1658320 - Harold
1660872 - Alex
1660877 - Alex
1660880 - Donghui
1660897 - Alex
1665398 - Alex
1665539 - Alex
1669228 - Alex

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

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