FlyBase December 2017

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 2015 - Nov 2016 (FB2015_61 - FB2016_06)

	Nov 14	Nov 15	% change	% of total genes
Total number of localized genes (excluding pseudogenes)	17382	17747	+2.1%
Localized genes with no GO annotation	4692	4941	-5.3%	27.8%
Localized genes with any GO annotation	12690	12806	+0.9%	73.0%
Localized genes with 1 or more term based on experimental evidence	6095	6724	+10.3%	37.8%
Localized genes with other non-IEA, non-ND evidence	3830	2420	-36.8%	13.6%
Localized genes with only IEA evidence	991	1864	+88.1%	10.5%
Localized genes with only ND evidence	1840	1798	-2.3%	10.1%

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

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

Notes: This year FlyBase has focussed on a major revision of its GO annotation set. Historic annotation sets (pre-2008) were reviewed for quality (i.e. correctness), traceability and adherence to current guidelines. Those sets that were deemed to not meet the criteria were removed. This included annotations made from conference abstracts, based on protein and DNA sequence records, various Celera project annotations, personal communications, FlyBase analysis 1992-. This saw over 10,000 annotations removed.

FlyBase is in the process of implementing a robust import pipeline to bring in external annotations on a sustainable basis. (Perviously this was only performed on an ad hoc basis.) This includes annotations from the GO PAINT project, which will fill many of the 'holes' left by the clean up of the annotation set.

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 historic GO annotation sets.

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.