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