FlyBase Progress Report for October 2008

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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

  1. Genes assigned by Reference Genome Project
  1. 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.