FlyBase December 2016

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1. Staff working on GOC tasks

Helen Attrill (GO curator/literature curator) 0.3 FTE

Giulia Antonazzo (GO curator/literature curator) 0.1 FTE

Alix Rey (GO curator/literature curator) 0.2 FTE

Steven Marygold (Literature curator) 0.1 FTE

Gillian Millburn (Literature curator) 0.2 FTE

Kathleen Falls (Developer)

Josh Goodman (Web Developer)

2. Annotation progress

Table showing progress in annotating Drosophila localized genes Nov 2015 - Nov 2016 (FB2015_06 - FB2016_05)

Nov 14 Nov 15 % change % of total genes
Total number of localized genes (excluding pseudogenes) 17382 17432 +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 2015 - Nov 2016 (FB2015_06 - FB2016_05)

November 2015 November 2016 % change
GO Biological Process (BP) annotations 48093 (8360 genes) 46131 (4879 genes) -4.1%
GO Molecular Function (MF) annotations 28273 (9121 genes)) 22742 (5393 genes) -4.1%
GO Cellular Component (CC) annotations 24219 (8360 genes) 21064 (2508 genes) -13.0%
Total annotations for localized genes 100585 89937 -10.6%

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. (2016). The Translation Factors of Drosophila melanogaster. Fly 10(4). DOI:10.1080/19336934.2016.1220464. PubMed PMID:27494710

Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ; FlyBase consortium. (2016). FlyBase: establishing a Gene Group resource for Drosophila melanogaster. Nucleic Acids Res. 44(D1):D786-D792. doi: 10.1093/nar/gkv1046 PubMed PMID:26467478.

b. Poster presentations

Biocuration 2016. April 2016: Gene Groups in 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:

B. Annotation Outreach and User Advocacy Efforts:

    • H. Attrill & G. Antonazzo attended the GO consortium meetings (Geneva, April & Los Angeles, Nov) and a LEGO training meeting (Hinxton UK, Aug/Sept)

C. Other:

    • H. Attrill, G. Antonazzo, Nick Brown awarded 5 year MRC funding for a grant which includes substantial GO content. Start date 1st April 2017. Nick is PI, Helen Co-I. G. Antonazzo will lead the development of pathway annotation and display in FlyBase using LEGO as a foundation for modeling.