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
(http://gocwiki.geneontology.org/index.php/Isa-complete_BP) 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
changes.
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,
Evelyn)
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
curators)
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)