Dec2006 ontology report

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Ontology Development & GO Editorial Office Report - December 2006

I. Ontology Development

  A. SourceForge
     1. Items opened    49
     2. Items closed    49
        a. GO Eds       17
        b. MOD curators 21*
        c. GO Ed/MOD collaborations     11**
     3. Items still open
        a. assigned, GO Eds       73
        b. assigned, MOD curators   22      
        c. unassigned    174

  *details in Appendix 1
  **details in Appendix 2

  B. The major item ins once again the is_a-complete biological
  process work (mainly David, Jane, Jen, Midori, Tanya; occasionally
  other curators). We have now frozen the "live" process ontology, and
  will commit the is_a-complete ontology immediately after the
  holidays. As noted last month, more detail is available on the
  internal wiki
  ( and in
  the Google spreadsheet.

  C. Collaboration with Jonathan Liu, MIT, also continues; based on
  his suggestions we have identified a few ontology changes to do once
  we "un-freeze." We're also looking into the possibility of meeting
  with him in early 2007, which could lead to a nice measurable set of

  D. GO editing informal tutorial plans -- see Meetings, in part 2.
  E. Other content items resolved
     1. High-level cellular component terms (Jane)
     2. Usual small things for diverse SF items

  F. Other content items in progress 
     1. Damaged DNA binding terms (Midori, with RefGen group,
        esp. Varsha & Eurie)
     2. Cardiac muscle terms, round 2 (Jen, with Varsha)
     3. Specific cytokine/interleukin production terms (Midori, Alex,
     4. General and specific transcription (Karen C, Midori, Val)
     5. Synaptic transmission (David)
     6. Several DNA repair items (Eurie)

David & Midori have imposed a bit of organization on the ontology
development main page in the internal wiki.

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

  A. OBO-Edit working group:
     1. OBO-Edit 1.1 beta testing really near completion (delayed by
        tricky bugs); target release by end 2006.
     2. "Question plugin" available for testing

  B. AmiGO working group (Jane, Amelia):
     1. AmiGO new look released (much work by Amelia)
     2. Documentation/user guide updated (Jane, Amelia, several MOD

  C. Software hub group (Jane, Amelia):
     1. AmiGO 2.0 features, continued; sample workflows on wiki

  D. Advocacy group (Jane):
     1. Calendar investigation
     2. SourceForge summary emails to be available to subscribers
        outside GOC

  E. Annotation outreach (Jen) (note: may overlap with Jen's group report)
     1. Follow-up to Aspergillus Annotation Jamboree
     2. More work on annotation SOP for wiki

  F. Conferences/meetings
     1. Preparation for Jan. 2007 GOC meeting
        a. Plans for a post-meeting hands-on session for curators to
        learn tips & tricks for GO editing, OBO-Edit, and GO CVS from
        the GO Eds

  G. Anything else
     1. GO Bibliography now has 1193 entries

Appendix 1: MOD curators' SF items
1568082 - Donghui, Tanya
1569614 - Donghui
1589483 - Donghui
1589610 - Donghui
1592307 - Rama
1598086 - Rama
1604808 - Donghui
1604814 - Donghui
1604823 - Donghui
1604835 - Donghui
1604874 - Donghui
1604902 - Donghui
1604923 - Donghui
1606243 - David
1606978 - David
1609295 - David
1609506 - David
1610358 - Donghui
1610449 - Donghui
1610463 - Donghui
1610471 - Donghui

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1493487 - Alex, Ruth
1521222 - David
1556522, 1558202 - Jodi
1573652 - Eurie, Varsha
1575217 - Eurie, Val
1578284 - Eurie, Varsha
1587269 - Alex
1605425 - Doug
1605707 - Alex
1613177 - Karen C

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