FlyBase December 2017

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1. Staff working on GOC tasks

Helen Attrill (GO curator/literature curator) 0.5 FTE

Giulia Antonazzo (GO curator/literature curator) 0.3 FTE

Phani Garapati (literature curator) 0.05 FTE

Silvie Fexova (literature curator) 0.05 FTE

Tamsin Jones (literature curator) 0.05 FTE

Vitor Trovisco (literature curator) 0.05 FTE

Kathleen Falls (Developer)

Josh Goodman (Web Developer)

2. Annotation progress

Table showing progress in annotating Drosophila localized genes Nov 2016 - Nov 2017 (FB2016_06 - FB2017_05)

Nov 16 Nov 17  % change  % of total genes
Total number of localized genes (excluding pseudogenes) 17432 17417 +0.1%
Localized genes with no GO annotation 4941 4520 -8.5% 26.0%
Localized genes with any GO annotation 12806 12554 +2.0% 72.1%
Localized genes with 1 or more term based on experimental evidence 6724 7682 +14.2% 44.1%
Localized genes with other non-IEA, non-ND evidence 2420 3641 +50.5% 21.0%
Localized genes with only IEA evidence 1864 1231 -33.4% 7.1%
Localized genes with only ND evidence 1798 1842 +2.4% 10.6%

Table showing total annotation progress for localized genes Nov 2016 - Nov 2017 (FB2016_06 - FB2017_05)

Nov 2016 Nov 2017  % change
GO Biological Process (BP) annotations 46131 (4879 genes) 52533 (13321 genes) 13.8%
GO Molecular Function (MF) annotations 22742 (5393 genes) 26882 (12530 genes) 18.2%
GO Cellular Component (CC) annotations 21064 (2508 genes) 25695 (11939 genes) 21.9%
Total annotations for localized genes 89937 105110 16.9%

Notes: This year FlyBase moved its primary GO curation over to Protein2GO (GOA). This has been very successful, enabling us to streamline the review of past GO annotation. As part of the import into the FlyBase Chado database, we have incorporated many other GO annotation sources including those generated via the PAINT project.

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. Reviewing the GO annotation for sets of genes related by shared functional or sequence characteristics 2. Reviewing the GO annotation for signaling pathways

4. Presentations and publications

a. Papers with substantial GO content

Marygold SJ, Attrill H, Lasko P. (2017). The Translation Factors of Drosophila melanogaster. Fly 10(4). DOI:10.1080/19336934.2016.1220464. PubMed PMID:27494710

b. Poster presentations

25th European Drosophila Research Conference, Sept 2017, London UK: Function-centered approaches for finding and analyzing genes within FlyBase. Helen Attrill, Giulia Antonazzo, Alix J. Rey, Kathleen Falls, Joshua L. Goodman, Gillian H . Millburn, Steven J. Marygold and the FlyBase Consortium.

5. Other Highlights:

A. Ontology Development Contributions:

    • H. Attrill & G. Antonazzo have contributed to the review of signaling pathways (Canonical Wnt and JAK/STAT, with K Van Auken & R. Lovering).

B. Annotation Outreach and User Advocacy Efforts:

    • H. Attrill & G. Antonazzo (FlyBase) and Val Wood & Midori Harris (PomBase) hosted the GO consortium signaling workshop and meeting (Cmabridge, Oct 2017)
    • Working groups: HTP (H. Attrill), Signaling (H. Attrill, G. Antonazzo)

C. Other:

    • H. Attrill, G. Antonazzo, Nick Brown started a 5 year MRC funding for a grant which includes substantial GO content on 1st April 2017.
    • FlyBase GO ribbons summaries implemented for FB2.0 beta site.