Sept2006 GO Ed report

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GO Editorial Office Report - September 2006

SourceForge items
  Items opened	59
  Closed by editorial office	46
   (note: 17 SF items closed outside GO-Ed. this month; see end of
    report for details and for non-GO-Ed contributors to items we
    closed)
  Items in progress, assigned to editorial office	71

The big jump in items closed outside GO-Ed is due to two factors: (1)
Alex committed the immunology revisions, which touched on several
items; and (2) SGD curators have resumed active editing.

Of the closed items, 5 came from reference genome annotation.

See monthly report in CVS for ontology statistics.

Erika's project:
  Erika has approval from her supervisors to work on 'response to
    drug' terms, and she's come up with a plan: GSK has a tool for
    identifying drugs of interest, which she'll use to figure out
    which substances should be represented in GO terms. She'll propose
    terms to Jen, who will do an initial check and then forward to
    other curators for additional comments. The usual GO procedures
    take over from there.
  Erika and her supervisor have also proposed a content meeting on
    muscle development, which would be held in Italy.
 
Content topics in progress (also see content wg below):
  is_a complete biological process
  PAMGO additions (Amelia)

Content topics resolved:
  Several small things for SourceForge items (mainly Midori)

Content working group update: 
  Progress on is_a complete biological process ontology at meeting in
    Seattle; summary on wiki
    (http://wiki.geneontology.org/index.php/Isa-complete_BP)
    (Jane, Jen, David Hill, Tanya Berardini)
  CNS development portion of biological process made is_a complete
    (David, Jen, Amelia)

OBO-Edit working group update:
  Confirm (and make small adjustments to) OBO-Edit 1.1 feature list
  OBO-Edit 1.1 beta release and testing cycle in progress
  OBO-Edit 1.2 features under discussion
    Improve the built-in reasoner
    Implement graph viewer-based editing
  Plan for curators to come up with editing-function wish list
  Early stages of planning a meeting on OBO-Edit (John, Chris)

AmiGO working group (Jane, Amelia):
  Testing for (slightly delayed) August release; release done
  Beginning work toward AmiGO as 'software hub'
  Gathering requirements & use cases
  Work on getting user feedback

Advocacy group (Jane):
  Quiet due to holidays

Annotation outreach (Jen):
  ARK-Genomics (see meetings below)
  New contacts:
    Atlantic Salmon
    Newly formed cow/sheep UK group.
  Annotation documentation for new groups in progress

Conferences/meetings
  GO External Advisory Board Meeting, Sept. 7, 2006, Seattle (Midori,
    Jane, Jen)
  MGED9, Sept 7-9, Seattle (Midori (8th-9th))
  Meeting to work on is_a complete biological process (see content wg
    above)
  GO Users Meeting, Sept. 10, Seattle (Midori, Jane, Jen)
  ARK-Genomics Meeting, Cambridge (Jen)
    Introduction to GO; AmiGO/GO web site demo; poster
  Planning for PAG outreach (Jen, with Rama, Trudy, Michelle, Fiona
    and Candace)

mesh2go mapping in progress (Jane)

Work on web pages (not yet live) (Amelia)
  Page reorganization and mock ups for new pages (e.g. the front page
    and current annotations page)
  Updating code and content to bring it up to web content
    accessibility guidelines
  Updating code for easier integration of AmiGO into the current
    website
  Updating out-of-date content (ongoing)

OBO work - adding ontologies and corresponding with various ontology
  submitters (Amelia)

Testing web conference software (Jen, Midori, Amelia)

Preparing grant to support immunology annotation (Jen, with Evelyn and
  others)

A few queries on the mailing lists (various people in and outside GO Ed.)

GO Bibliography now has 1063 entries (hooray for the PLoS full text
  search)


Appendix 1: Items closed outside GO-Ed this month

1031159, 1301814, 1371824, 1489769, 1513908, 1513909, 1526292 -
  content by Alex Diehl, Amelia Ireland, and immunology content
  meeting participants; for 1031159, Suparna Mundodi, Michelle Gwinn,
  Tanya Berardini also involved; edits done by Alex & Amelia; items
  closed by Alex

1527944 - Julie Park
1544157 - content by Karen Christie, Eurie Hong, Varsha Khodiyar;
	  edits done by Karen Christie
1546289 - content by Julie Park, Karen Christie; edits done by Karen
	  Christie
1549220 - content by Eurie Hong, Midori Harris; edits done by Karen
	  Christie
1556745 - content by Karen Christie, Eurie Hong, Val Wood; edits done
	  by Karen Christie
1557003 - content by Val Wood, Karen Christie; edits done by Karen
	  Christie
1562934 - content by David Hill; edits by Harold Drabkin
1562981 - content by David Hill, Tanya Berardini, Midori Harris, Karen
	  Christie; edits done by Karen Christei
1563159 - content by Eurie Hong; edits done by Karen Christie
1565282 - Karen Christie
1565292 - content by Karen Christie, Midori Harris; edits done by
          Karen Christie


Appendix 2: input from others on SF items closed this month
1425417 - Rob Nash
1427790 - David Hill, Doug Howe, Harold Drabkin, Karen Christie
1438187 - David Hill, Becky Foulger
1481900 - Doug Howe
1493875 - Karen Christie, Val Wood, Pascale Gaudet
1532264 - Rama Balakrishnan, Val Wood
1548729 - Karen Christie, Pascale Gaudet
1553364 - Varsha Khodiyar, David Hill, Eurie Hong
1563799 - Doug Howe
1566423 - Alex Diehl