FlyBase Progress Report for October 2008
Staff:
Susan Tweedie (1 FTE on GO funded by MRC UK)
Michael Ashburner
Annotation Progress
Table showing current status of Drosophila GO annotations in October 2008
Biological Process | Molecular Function | Cellular Component | Combined GO | |
---|---|---|---|---|
Genes with any GO annotation | 8080 | 9253 | 6893 | 10131 |
Genes with > 1 experimentally based term | 2603 | 1217 | 1403 | 3163 |
Genes with only IEA | 2288 | 2055 | 1684 | 1716 |
Genes with only ND | 855 | 859 | 1013 | 728 |
Table showing annotation progress since the start of the Reference Genome project in August 2006
August 2006 | October 2008 | % change | |
---|---|---|---|
Experimental evidence | 11888 | 17322 | +46% |
Computational evidence | 14946 | 15487 | +4% |
Author/curator statements | 16711 | 16506 | -1% |
Electronic annotation | 22626 | 16010 | -29% |
No biological data available | 4997 | 5022 | +0.5% |
Total annotations | 71168 | 70351 | -1% |
Methods and strategies for annotation
Literature curation:
Almost 100% of curation effort is devoted to capturing GO terms from published literature.
Priorities for annotation
- Genes assigned by Reference Genome Project
- Genes that lack any annotation
Computational annotation strategies:
The only computational strategy used is based on the mapping to InterPro domains. This is updated for each release of FlyBase (every 4-6 weeks).
Presentations and Publications
a. Papers with substantial GO content
Tweedie, S., Ashburner, M., Falls.,K., Leyland,P ., McQuilton, P., Marygold, S., Millburn, G., Osumi-Sutherland, D., Schroeder, A., Seal, R., Zhang, H., and the FlyBase Consortium. FlyBase: Enhancing Drosophila Gene Ontology (GO) annotations. Nucleic Acids Res. [in press]
b. Presentations including Talks and Tutorials and Teaching
c. Poster presentations
Susan Tweedie, The FlyBase Consortium and The Gene Ontology Consortium. Drosophila melanogaster: a GO reference genome. 49th Drosophila Research Conference April 2-6 2008 San Diego, CA.
Other Highlights:
A. Ontology Development Contributions:
- S. Tweedie contributed to the project identifying terms that should be limited to specific taxa.
B. Annotation Outreach and User Advocacy Efforts:
- S. Tweedie is a member of the GO newsletter 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-Jamborees (July and October 2008)
C. Other:
Terms predicted by electronic annotation have been reviewed. All terms assigned more than one year ago have now been removed (this will become public in Novemberr 2008). All IEA-based terms now come solely from InterPro to GO mappings.