Nov2007 ontology report

Ontology Development & GO Editorial Office Report - November 2007

I. Ontology Development

• SourceForge
  • Items opened: 74
  • Items closed: 46
    • GO Eds: 28
    • MOD curators: 4 (details in Appendix 1)
    • GO Ed/MOD collaborations: 14 (details in Appendix 2)
  • Items still open: 279
    • assigned, GO Eds: 43
    • assigned, MOD curators: 63
    • unassigned: 173

• Several SourceForge items resolved

• Content items in progress
  • content meeting on lung development to be held December 5-6 (http://wiki.geneontology.org/index.php/Lung_Development)
  • Work has resumed on sensu terms; see http://gocwiki.geneontology.org/index.php/Meeting_Notes_3
  • David and Tanya are almost finished with Chris' file of "regulation of non-process" anomalies (details at http://gocwiki.geneontology.org/index.php/Regulation_Main_Page, especially http://gocwiki.geneontology.org/index.php/Part_3
  • Erika has, with Jen, resumed work on the 'response to drug' revamp (http://gocwiki.geneontology.org/index.php/Response_to_drug)
  • Addition of enzyme activity terms from EC has resumed (Midori, Colin Batchelor)
  • More synonyms for enzyme activity terms added, derived from IntEnz (Midori, Colin Batchelor)
  • Various SourceForge items

• Erika and Jen are preparing a manuscript on the muscle content meeting

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

• Jane on maternity leave
• Amelia visiting Berkeley database/software group

• OBO-Edit working group:
  • Additional OBO-Edit 2.0 betas released; much testing going on, in the hope of releasing before John leaves
  • Jen has begun contributing to OBO-Edit programming

• Advocacy/outreach group (Jane; Jen while Jane is away):
  • Annotation
    • Jen and Pascale discussing roles of Reference Genome and Annotation Outreach groups
    • Discussions with Tsai-Tien Tsengon GO transport(er) terms, TCDB, and annotations (Jen, Michelle, PIs)
    • Continued discussion with Giorgio Valle and Erika on grape annotation
  • Community
    • November newsletter released
    • GOC publications, talks, etc. now collected on wiki (http://gocwiki.geneontology.org/index.php/Publications%2C_tutorials%2C_talks%2C_posters)
    • Usual gohelp traffic

• Conferences/meetings
  • EMBRACE (EU "network of excellence") workshop on Applied GO, Nov. 7-9, Bari, Italy
    • Talks on GO (Midori) and GOA (Emily); AmiGO tutorial (Midori, Erika)
  • Preparation for lung development content meeting - Jen will edit remotely

• Anything else
  • NAR database issue manuscript published online Nov. 4th
  • GO bibliography has 1680 entries

Appendix 1: MOD curators' SF items
1815288 Tanya, David
1824802 Tanya, David, Pascale
1831939 Doug, David
1840573 Tanya

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
1418820 MANY GOC curators
1748527 Doug, transporter group
1757824 David, Chris
1823408 Val
1825979 Val, Rama
1826071 Val
1828976 Val, Kirill
1830458 Karen C, Val
1831218 Alex
1834020 Peter
1834076 Val
1834732 Jodi, Varsha
1835816 Alex
1836332 Karen C

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

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