Feb2006 GO Ed report

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GO Editorial Office Report - February 2006

SourceForge items
  Items opened	75
  Closed by editorial office	53
   (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
- Our visiting student, Erika, has made lots of progress learning the
ways of GO curation. She has established a good working relationship
with the neurobiology interest group, and made a number of additions
and changes in the process ontology for nervous system development and
functioning. She is also learning GOA's annotation procedures (with
Emily Dimmer), and has started annotating glutamate receptors.

- The GO office (both GO Eds and GOA) spent a day helping Jacqui
White, who has recently joined Sanger to work on their mouse knockout
project (see http://www.sanger.ac.uk/Teams/Team109/). She's been
charged with choosing genes for the project to knock out, and was/is
interested in using GO to help with the target selection. At some
point she may also become interested in PATO's doings, since they'll
need to document the knockout phenotypes.

Content topics in progress:
  Sensu terms - ongoing discussion in GOC (from GO Eds, mainly Jen)
  MetaCyc and GO consistency (includes metacyc2go mapping) (Amelia,
    with TAIR curators, esp. Peifen Zhang and Christophe Tissier)
  Neurogenesis (Erika, with Jen and the neurobiology interest group)
  Neurotransmitter uptake and secretion (Erika, with Jen and the
    neurobiology interest group)
  Plant development terms (Jen, with TAIR curators and Pankaj Jaiswal)

Content topics resolved:
  Several nervous system-related development terms (Erika, with Jen
    and the neurobiology interest group)
  Several small things for SourceForge items

OBO-Edit working group update: 
  Highlight: The 'webinar' held Feb. 7-8 was a huge success (despite
    two out of three technologies falling over due to the number of
    participants). Transcripts are available in the group mailing list
    archives, and will probably also be put on the web somewhere. We
    may run similar tutorial sessions in the future, and ...
  Inspired by the webinar success, we have instigated regular
    'meetings' via IRC (and John is looking into other technological
    possibilities). These can include shorter demos of new (or old but
    underappreciated) features, cross-platform testing, discussions,
    etc.
  Decided that version 1.000-beta16 will be eligible for release once
    the User Guide is complete.
  Progress on test suites, both automated (John D-R) and manual
    (curators; compiled by Jen and Amelia)
  Looking into making tutorial 'movies' like this one from RCSB:
    http://www.rcsb.org/pdb/

Conferences/meetings
  GO tutorial (annotation, microarray analysis) at MUGEN course, Milan
    (Jane)
  Preparation for GO talk and tutorial for computing workshop at
    European Fission Yeast Meeting (Hinxton, mid-March) (Jane, Midori)
  A little bit more progress planning GO Users meeting at MGED9 - room
    booked for Sept. 10th (Midori)
  Posters for St. Croix meeting (all)

Publication
  Book chapter in progress: 'Parasites and GO' for bioinformatics text
    book for parasitologists (Jane, with Matt Berriman)

Annotation outreach (Jen)
  Submission of annotations by PseudoCAP (with David Hill, Emily Dimmer)

AmiGO working group
    Conference call (Amelia, Jane)
    Web page mockups (Amelia)

Some updates to documentation (Amelia, Jen)

Some updates to web pages (Amelia)

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

The GO Bibliography now has 773 entries.


Appendix 1: input from others on SF items closed this month
1382483 - Katica Ilic
1416285 - David Hill, Doug Howe
1334217 - David Hill, Doug Howe
1431624 - Becky Foulger, David Hill
1420504 - David Hill
1429280 - David Hill
1429350 - Becky Foulger, Doug Howe
1242580 - TAIR curators
1416461 - David Hill, Doug Howe
1415524 - Doug Howe
1237567 - Pascale Gaudet, Michelle Gwinn
1228979 - Russ Collins, David Hill
1012287 - Russ Collins, David Hill, Pankaj Jaiswal
1247046 - TAIR curators

Appendix 2: SF items that touch on other OBO ontologies
1416285 - CL
1428581 - CL
1416461 - CL