Nov2006 ontology report

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Ontology Development & GO Editorial Office Report - November 2006

I. Ontology Development

  A. SourceForge
     1. Items opened	91
     2. Items closed	97
        a. GO Eds	53
	b. MOD curators	38*
	c. GO Ed/MOD collaborations	6**
     3. Items still open
        a. assigned, GO Eds	  74
	b. assigned, MOD curators	  22
	c. unassigned	 174

  *details in Appendix 1
  **details in Appendix 2

  B. Considerable progress on is_a-complete biological process (mainly
  David, Jane, Jen, Midori, Tanya; occasional contributions from other
  curators on specific questions). Much more detail is available on
  the internal wiki:
  http://gocwiki.geneontology.org/index.php/Isa-complete_BP. There is
  also a Google spreadsheet of outstanding tasks and questions.

  C. Collaboration with Jonathan Liu, MIT: David has pointed Jonathan
  to the is_a-complete file. David & Midori commented on the most
  recent set of suggestions; as noted in the last managers' call, "too
  specific" terms tend to need work, whereas "too general" terms often
  serve some ontology-organization purpose. David will suggest to
  Jonathan that he compare different versions of the is_a-complete
  file to see how the analysis results change.

  D. Erika's work on 'response to drug' revamp also documented on
  wiki: http://gocwiki.geneontology.org/index.php/Response_to_drug
 
  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)

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 near completion; target release
        date Dec. 14
     2. Reviews received for Bioinformatics Application Note
        manuscript; Chris & John will respond to editors
     3. obomerge testing continues; also relevant to is_a-complete
        ontology work (Jane)

  B. AmiGO working group (Jane, Amelia):
     1. Finalizing new look (Amelia)
     2. Documentation/user guide for next release

  C. Software hub group (Jane, Amelia):
     1. AmiGO 2.0 features

  D. Advocacy group (Jane):
     1. November newsletter sent
     2. GOhelp list a little bit more active than in Oct.

  E. Annotation outreach (Jen) (note: may overlap with Jen's group report)
     1. Aspergillus Annotation Jamboree (also see meetings)
     2. More progress populating outreach database
     3. Annotation SOP for wiki

  F. Conferences/meetings
     1. Aspergillus Annotation Jamboree, Copenhagen (Jen)
     2. Topic contributions for Jan. 2007 GOC meeting

  G. Anything else
     1. mesh2go mapping (Jane)
     2. GO Bibliography now has 1146 entries


Appendix 1: MOD curators' SF items
1237491 - Erika
1240327 - Erika
1459883 - Erika
1511520 - David
1569577 - Karen C
1573845 - David
1575421 - David
1584578 - David
1587343 - David
1588923 - Donghui
1588926 - Donghui
1588927 - Donghui
1588931 - Donghui
1588993 - Donghui
1589002 - Donghui
1589006 - Donghui
1589008 - Donghui
1589417 - Donghui
1589420 - Donghui
1589483 - Donghui
1589610 - Donghui
1595911 - Donghui
1589668 - Donghui
1589666 - Donghui
1589662 - Donghui
1589604 - Donghui
1589600 - Donghui
1589286 - David
1589469 - Donghui
1604808 - Donghui
1604814 - Donghui
1604823 - Donghui
1604827 - Donghui
1604835 - Donghui
1604874 - Donghui
1604902 - Donghui
1604923 - Donghui
1605436 - David

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
 907476 - Val
1493227 - Pascale
1567822 - Alex
1569608 - Kimberly
1587325 - Emily, David, Rama
1595591 - David

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