FlyBase November 2010

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1. Staff working on GOC tasks

Susan Tweedie (GO curator) 1 FTE

Peter McQuilton (Literature curator) 0.1 FTE

Steven Marygold (Literature curator) 0.05 FTE

Gillian Millburn (Literature curator) 0.1 FTE

David Osumi-Sutherland (Literature curator) 0.025 FTE

Raymund Stefancsik (Literature curator) 0.1 FTE

Total number of staff working on GOC tasks 1.375; total funded by NIH GO grant 0.

2. Annotation progress

Table showing progress in annotating Drosophila protein coding genes Oct 2008 - Dec 2009

Oct 08 Dec 09  % change  % of total genes
Protein coding genes with any GO annotation 10131 10830 +7% 78%
Protein coding genes with 1+ experimentally based term 3163 3589 +13% 26%
Protein coding genes with other non IEA, ND evidence 4524 4085 -10% 30%
Protein coding genes with only IEA 1716 1776 +3% 13%
Protein coding genes with only ND 728 1435 +97% 10%

Note there are 13807 predicted protein coding genes in Drosophila (FlyBase release FB2009_10) GO annotation is available for an additional 344 genes that encode RNA products and 2046 genes that are not localised to the genome.

Table showing annotation progress since the start of the Reference Genome project in August 2006

August 2006 October 2008 December 2009  % change since Oct 2008
Experimental evidence 11888 17322 20039 +16%
Computational evidence 14946 15487 15352 -1%
Author/curator statements 16711 16506 16366 -1%
Electronic annotation 22626 16010 15083 -6%
No biological data available 4997 5022 4992 -0.6%
Total annotations 71168 70351 71832 +2%

Note this table includes annotations for genes that have not yet been localized to the genome.

Biological Process - 32031 Molecular Function - 24543 Cellular Component - 15262

3. Methods and strategies for annotation

a. Literature curation:

b. Computational annotation strategies: GO annotation based on InterPro2GO mappings are updated with every release of FlyBase.

c. Priorities for annotation:

  1. Literature associated with Reference Genome genes.
  2. Literature describing the characterization of genes that currently lack GO annotation.

4. Presentations and publications

GO 2009 Publications, Tutorials & Workshops, Presentations, Posters, and Resources

5. Other Highlights:

A. Ontology Development Contributions:

    • S. Tweedie participated in the heart development content meeting held at UCL September 22, 2009
    • S. Tweedie is part of the group reviewing signaling terms.

B. Annotation Outreach and User Advocacy Efforts:

    • S. Tweedie is a member of the GO news team and monitored the news desk submissions in Aug and Sept 2009.
    • S. Tweedie answers user GO related questions from the FlyBase and GO help email lists.
    • S. Tweedie participated in the Reference Genome curation e-Jamborees (February and October 2009)

C. Other:

FlyBase revamped the GO section of their gene report pages:

    • Terms based on experimental evidence are now presented separately from other evidence types
    • The source of GO annotations from external groups is now acknowledged
    • The majority of 'with' objects are now linked-out
    • ND annotations have been replaced with an explicit statement that there is no there is no data available to support a specific term as of a given date.

FlyBase also has changed the way GO annotations are used to describe functional information about a gene in the summary section of the gene report; terms assigned by experimental evidence are now shown in preference to other evidence types if available.