FlyBase, September 2009

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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 - Sept 2009

Oct 08 Sept 09 % change % of total genes
Protein coding genes with any GO annotation 10131 10149 +0.2% 73%
Protein coding genes with 1+ experimentally based term 3163 3508 +11% 25%
Protein coding genes with other non IEA, ND evidence 4524 4179 -7.5% 30%
Protein coding genes with only IEA 1716 1726 +0.6% 12.5%
Protein coding genes with only ND 728 736 +1.1% 5.3%

Note there are 13825 predicted protein coding genes in Drosophila (FlyBase release FB2009_08)

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

August 2006 October 2008 September 2009 % change since Oct 2008
Experimental evidence 11888 17322 19781 +15%
Computational evidence 14946 15487 15496 0%
Author/curator statements 16711 16506 16393 -0.7%
Electronic annotation 22626 16010 15612 -2.5%
No biological data available 4997 5022 4995 -0.5%
Total annotations 71168 70351 72277 +2.7%

Note this table includes annotations for genes 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

a. Papers with substantial GO content:

The Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species. PLoS Comput Biol 5(7): e1000431. doi:10.1371/journal.pcbi.1000431

b. Presentations including Talks and Tutorials and Teaching:

FlyBase/FlyMine 1 day workshop - Dept. of Genetics, University of Cambridge, UK (Peter McQuilton) May 29th 2009

c. Poster presentation:

Improving functional annotation of Drosophila transcription factors in FlyTF and FlyBase. Third International Biocuration Conference, Berlin, Germany. Susan Tweedie, Ulrike Pfreundt and Boris Adryan FlyBase-Cambridge, Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, UK (April 16-19th 2009)