FlyBase, March 2010
From GO Public
Contents |
1. Staff working on GOC tasks
Susan Tweedie (GO curator) 1 FTE
Stephanie Bunt (Literature curator) 0.05 FTE
Simon Reeve (Literature curator) 0.025 FTE
Peter McQuilton (Literature curator) 0.05 FTE
Steven Marygold (Literature curator) 0.025 FTE
Gillian Millburn (Literature curator) 0.1 FTE
Raymund Stefancsik (Literature curator) 0.05 FTE
Total number of staff working on GOC tasks 1.3 FTE; total funded by NIH GO grant 0.
2. Annotation progress
Table showing progress in annotating Drosophila protein coding genes Oct 2008 - Mar 2010
| Oct 08 | Sep 09 | Mar 10 | % change | % of total protein coding genes | |
|---|---|---|---|---|---|
| Protein coding genes with any GO annotation | 10131 | 10149 | 10206 | +0.6% | 74.4% |
| Protein coding genes with 1+ experimentally based term | 3163 | 3508 | 3629 | +3.5% | 26.4% |
| Protein coding genes with other non IEA, ND evidence | 4524 | 4179 | 4096 | -2.0% | 29.9% |
| Protein coding genes with only IEA | 1716 | 1726 | 1695 | -1.7% | 12.5% |
| Protein coding genes with only ND | 728 | 736 | 786 | +6.8% | 5.7% |
Note there are 13721 predicted protein coding genes in Drosophila (FlyBase release FB2010_03)
Table showing annotation progress since the start of the Reference Genome project in August 2006
| August 2006 | October 2008 | September 2009 | March 2010 | % change since September 2009 | |
|---|---|---|---|---|---|
| Experimental evidence | 11888 | 17322 | 19781 | 21193 | +7.1% |
| Computational evidence | 14946 | 15487 | 15496 | 15474 | -0.1% |
| Author/curator statements | 16711 | 16506 | 16393 | 16342 | -0.3% |
| Electronic annotation | 22626 | 16010 | 15612 | 15181 | -2.8% |
| No biological data available | 4997 | 5022 | 4995 | 5427 | +8.6% |
| Total annotations | 71168 | 70351 | 72277 | 73617 | +1.9% |
Note this table includes annotations for genes encoding RNA and 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
None since Dec 2009.
5. Other Highlights:
A. Ontology Development Contributions:
- S. Tweedie participated in the kidney development content meeting held at EBI Jan 25th, 2010
- 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.
- S. Tweedie answers user GO related questions from the FlyBase and GO help email lists.
- S. Tweedie participated in the Reference Genome curation e-Jamboree (February 2010)
