FlyBase December 2010

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1. Staff working on GOC tasks

Susan Tweedie (GO curator) 1 FTE

Stephanie Bunt (Literature curator)

Peter McQuilton (Literature curator)

Steven Marygold (Literature curator)

Gillian Millburn (Literature curator)

Raymund Stefancsik (Literature curator)

Kathleen Falls (Developer)

Andy Schroeder (Developer)

Total number of staff working on GOC tasks approx 1.5 FTE; total funded by NIH GO grant 0.

2. Annotation progress

Table showing progress in annotating Drosophila protein coding genes Nov 2009 - Nov 2010 (FB2009_09 - FB2010_09)

Nov 09 Nov 10  % change  % of total genes
Protein coding genes with any GO annotation 10097 10325 +2.3% 74.7%
Protein coding genes with 1+ experimentally based term 3511 3994 +13.8% 28.8%
Protein coding genes with other non IEA, ND evidence 4159 3847 -7.5% 27.8%
Protein coding genes with only IEA 1693 1713 +1.2% 12.4%
Protein coding genes with only ND 734 771 +4.8% 5.6%

Note there are 13827 predicted protein coding genes in Drosophila (FlyBase release FB2010_09 - November 19th 2010) GO annotation is available for an additional 340 genes that encode RNA products and 2085 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 November 2009 November 2010  % change since Nov 2009
Experimental evidence 11888 17322 20057 24115 +20.2%
Computational evidence 14946 15487 15493 15493 0%
Author/curator statements 16711 16506 16379 16308 -0.4%
Electronic annotation 22626 16010 14923 15641 +4.8%
No biological data available 4997 5022 4992 5422 +8.6%
Total annotations 71168 70351 71844 76979 +7.1%

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

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

Publications,_Talks,_Posters_2010-

5. Other Highlights:

A. Ontology Development Contributions:

    • S. Tweedie participated in the kidney development content meeting held at Hinxton Jan, 2010 and S. Bunt helped review the insect kidney terms from this meeting.

B. Annotation Outreach and User Advocacy Efforts:

    • S. Tweedie is a member of the GO news team.
    • S. Tweedie joined the GO help desk rota and answered addition help request relevant to Drosophila.
    • S. Tweedie participated in the GO Annotation Workshop (Geneva, June 16-18 2010)
    • S. Tweedie attended the GO consortium meeting (Bar Harbor, Sept 7-9 2010)

C. Other:

    • Annotations for genes involved in hearing were reviewed in collaboration with Guvanch Ovezmyradov from the Auditory GO Annotation (AGOA) group. Revised annotations were added to FlyBase in release FB2010_09 (November 2010).