FlyBase November 2010
- 1 1. Staff working on GOC tasks
- 2 2. Annotation progress
- 3 3. Methods and strategies for annotation
- 4 4. Presentations and publications
- 5 5. Other Highlights:
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 - Dec 2009
|Oct 08||Dec 09||% change||% of total genes|
|Protein coding genes with any GO annotation||10131||10830||+7%||78%|
|Protein coding genes with 1+ experimentally based term||3163||3589||+13%||26%|
|Protein coding genes with other non IEA, ND evidence||4524||4085||-10%||30%|
|Protein coding genes with only IEA||1716||1776||+3%||13%|
|Protein coding genes with only ND||728||1435||+97%||10%|
Note there are 13807 predicted protein coding genes in Drosophila (FlyBase release FB2009_10) GO annotation is available for an additional 344 genes that encode RNA products and 2046 genes that are not localised to the genome.
Table showing annotation progress since the start of the Reference Genome project in August 2006
|August 2006||October 2008||December 2009||% change since Oct 2008|
|No biological data available||4997||5022||4992||-0.6%|
Note this table includes annotations for genes that have not yet been localized to the genome.
Biological Process - 32031 Molecular Function - 24543 Cellular Component - 15262
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
5. Other Highlights:
A. Ontology Development Contributions:
- S. Tweedie participated in the heart development content meeting held at UCL September 22, 2009
- 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 and monitored the news desk submissions in Aug and Sept 2009.
- 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 (February and October 2009)
FlyBase revamped the GO section of their gene report pages:
- Terms based on experimental evidence are now presented separately from other evidence types
- The source of GO annotations from external groups is now acknowledged
- The majority of 'with' objects are now linked-out
- ND annotations have been replaced with an explicit statement that there is no there is no data available to support a specific term as of a given date.
FlyBase also has changed the way GO annotations are used to describe functional information about a gene in the summary section of the gene report; terms assigned by experimental evidence are now shown in preference to other evidence types if available.