FlyBase, September 2009
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)