Jan2006 GO Ed report

GO Editorial Office Report - January 2006

SourceForge items
  Items opened	66
  Closed by editorial office	62
   (note: no SF item 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	74

See monthly report in CVS for ontology statistics.

Highlights

- Erika Feltrin arrived on Jat. 16th. She's a PhD student in Giorgio
Valle's group at the University of Padova, Italy, and will be visiting
us for six months. With guidance from all of us, but especially Jen,
she's learning how we work and contributing to content in areas
related to neurobiology. (David Hill and Doug Howe have already been
involved in some discussions via SorceForge.) She'll probably also
work on some signaling pathways in GO, and will look at relevant bits
of Reactome, interact with at least one of the Reactome curators here.

- With John Day-Richter and several MOD curators, we have formed the
OBO-Edit working group. The group is in the process of drafting
improved beta-testing and release procedures, and setting priorities
for OBO-Edit development. We've therefore also been doing quite a bit
of beta-testing.

Content topics in progress:
  Cell differentiation (Jen, with Erika)
  Cell cycle (Amelia, with Val Wood, PSU)
  MetaCyc and GO consistency (includes metacyc2go mapping) (Amelia,
    with TAIR curators, esp. Peifen Zhang and Christophe Tissier)
  Moving unlocalized protein complexes (children of GO:0005941) to
    locations, and writing defs for them (Jane)

Content topics resolved:
  Complete is_a paths for cellular component (Jane, with Chris M)
  Metamorphosis (Jen, with others including MA, Russ Collins, FB)
  Several small things for SourceForge items  

Conferences/meetings
  Plant & Animal Genomes XIV (Jen)
   - Organized full-day workshop on GO, with Harold Drabkin, Rama
     Balakrishnan (others?); report submitted separately
     (note: conference calls proved useful for organizing)
   - Spoke at Development and Implemention of Ontologies in the
     Database workshop
   - Some follow-up queries
  Preparation for GO tutorial at MUGEN course in Feb (Jane)
  A modicum of progress planning GO Users meeting at MGED9 (Midori)

Paperwork and some small contributions to content for grant (Midori,
   Jane)

Mips2go mapping finished at last! (Jane)

Annotation outreach (Jen)
  Fiona Brinkman's group
  Affymetrix
  Ensembl

Some updates to documentation (Amelia, Midori)

Some updates to web pages (Amelia)

Scripts (Amelia)

A few queries on the mailing list (Midori, Jane)

The GO Bibliography now has 730 entries. Sue Rhee has looked through
the 'other uses' category and suggested new categories; based on her
suggestions, we (Midori and Amelia) have created four new categories
and updated scripts accordingly. We're now waiting for Mike C to
deploy the updated biblio.cgi script. The new categories are:

  - use of GO in clinical applications
  - use of GO in network modeling and analysis
  - use of GO in comparative genomics and evolutionary analysis
  - use of GO to support predictions
    (i.e. predicting something other than GO annotations)

 
Appendix: input from others on SF items closed this month
1232708 - Rama Balakrishnan, Kimberly Van Auken, Val Wood
1358995 - Alex Diehl, Harold Drabkin, Duncan Legge
1369320 - Val Wood