FlyBase December 2015

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1. Staff working on GOC tasks

Helen Attrill (GO curator/literature curator) 0.35 FTE

Giulia Antonazzo (GO curator/literature curator) 0.25 FTE

Alix Rey (GO curator/literature curator) 0.2 FTE

Pepe Urbano (Outreach)

Steven Marygold (Literature curator)

Gillian Millburn (Literature curator)

Raymund Stefancsik (Literature curator)

Laura Ponting (Literature curator)

Kathleen Falls (Developer)

Andy Schroeder (Developer)

Josh Goodman (Web Developer)


2. Annotation progress

Table showing progress in annotating Drosophila localized genes Nov 2014 - Nov 2015 (FB2014_06 - FB2015_05)

Nov 14 Nov 15 % change % of total genes
Total number of localized genes (excluding pseudogenes) 17382 17406 +0.14%
Localized genes with no GO annotation 4692 4449 -5.0% 25.6%
Localized genes with any GO annotation 12690 12947 +2.0% 74.4%
Localized genes with 1 or more term based on experimental evidence 6095 9727 +59.6% 55.9%
Localized genes with other non-IEA, non-ND evidence 3746 3830 +2.2% 22.0%
Localized genes with only IEA evidence 1074 991 -7.7% 5.7%
Localized genes with only ND evidence 1775 1840 +3.7% 10.6%

Table showing total annotation progress for localized genes Nov 2014 - Nov 2015 (FB2014_06 - FB2015_05)

November 2014 November 2015 % change
GO Biological Process (BP) annotations 46245 (9471 genes) 48093 (8360 genes) +4.0% (+2.6%)
GO Molecular Function (MF) annotations 27872 (9037 genes) 28273 (9121 genes) +1.4% (+0.9%)
GO Cellular Component (CC) annotations 22911 (7959 genes) 24219 (8360 genes) +5.7% (+5.0%)
Total annotations for localized genes 97028 100585 +3.7%

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.  Targeting unannotated Drosophila Melanogaster genes with human orthologs associated with disease (via OMIM mapping)
  2. Reviewing the GO annotation for sets of genes related by shared functional or sequence characteristics or within macromolecular complexes.

4. Presentations and publications

a. Paper with substantial GO content

Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ; FlyBase consortium. FlyBase: establishing a Gene Group resource for Drosophila melanogaster. Nucleic Acids Res. 2015 Oct 13. pii: gkv1046. doi: 10.1093/nar/gkv1046 PubMed PMID:26467478.

b. Presentations including Talks and Tutorials and Teaching

56th Annual Drosophila Research Conference. March 2015: Gene Groups in FlyBase. Steven Marygold, Helen Attrill, FlyBase consortium.

c. Poster presentations

56th Annual Drosophila Research Conference. March 2015: Gene Groups in FlyBase. Steven Marygold, Helen Attrill, FlyBase consortium.

5. Other Highlights:

A. Ontology Development Contributions:

B. Annotation Outreach and User Advocacy Efforts:

    • H. Attrill & Giulia Antonazzo attended the GO consortium meeting (Washington 2015)

C. Other:

    • Giulia Antonazzo (March 2015) & Pepe Urbano (June 2015) replaced Susan Tweedie on an MRC grant.