FlyBase December 2014

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1. Staff working on GOC tasks

Susan Tweedie (GO curator) 0.8 FTE

Helen Attrill (GO curator/literature curator) 0.35 FTE

Peter McQuilton (Literature curator)

Steven Marygold (Literature curator)

Gillian Millburn (Literature curator)

Raymund Stefancsik (Literature curator)

Kathleen Falls (Developer)

Andy Schroeder (Developer)

Total number of staff working on GOC tasks approx 1.5 FTE; total funded by NIH GO grant 0.

2. Annotation progress

Table showing progress in annotating Drosophila localized genes Nov 2013 - Nov 2014 (FB2013_06 - FB2014_06)

Nov 13 Nov 14 % change % of total genes
Total number of localized genes (excluding pseudogenes) 16457 17382 +5.6%
Localized genes with no GO annotation 4655 4692 +0.8% 27.0%
Localized genes with any GO annotation 11802 12690 +7.5% 73.0%
Localized genes with 1 or more term based on experimental evidence 5786 6095 +18.8% 35.1%
Localized genes with other non-IEA, non-ND evidence 3733 3746 +0.4% 21.5%
Localized genes with only IEA evidence 1270 1074 -15.4% 6.2%
Localized genes with only ND evidence 1013 1775 +75.2% 10.2%

Table showing total annotation progress for localized genes Nov 2013 - Nov 2014 (FB2013_06 - FB2014_06)

November 2013 November 2014 % change
GO Biological Process (BP) annotations (genes annotated for non-ROOT BP term) 42546 (9183 genes) 46245 (9471 genes) +8.7% (+3.1%)
GO Molecular Function (MF) annotations (genes annotated for non-ROOT MF term) 26126 (8870 genes) 27872 (9037 genes) +6.7% (+1.9%)
GO Cellular Component (CC) annotations (genes annotated for non-ROOT CC term) 20294 (7507 genes) 22911 (7959 genes) +4.8% (+6.0%)
Total annotations for localized genes 88966 97028 +8.6%

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.  Genes that currently lack GO annotation.
  2. Reviewing GO annotation for groups of related genes

4. Presentations and publications

a. Paper with substantial GO content

1. Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z. Overview of the gene ontology task at BioCreative IV. Database (Oxford). 2014 Aug 25;2014. pii: bau086. doi: 10.1093/database/bau086. PubMed PMID:25157073; PubMed Central PMCID:PMC4142793.

2. Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJ, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z. BC4GO: a full-text corpus for the BioCreative IV GO task. Database (Oxford). 2014 Jul 28;2014. pii: bau074. doi: 10.1093/database/bau074. PubMed PMID:25070993; ; PubMed Central PMC4112614.

3. Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP. Representing kidney development using the gene ontology. PLoS One. 2014 Jun 18;9(6):e99864. doi: 10.1371/journal.pone.0099864. eCollection 2014. PubMed PMID: 24941002; PubMed Central PMCID: PMC4062467.

b. Presentations including Talks and Tutorials and Teaching

c. Poster presentations

55th Annual Drosophila Research Conference. March 2014: Gene Groups in FlyBase. H. Attrill, S.J. Marygold, S. Tweedie and the FlyBase Consortium.

5. Other Highlights:

A. Ontology Development Contributions:

B. Annotation Outreach and User Advocacy Efforts:

    • S. Tweedie and H. Attrill attended the GO consortium meeting (Barcelona, 2014)

C. Other:

    • S. Tweedie left FlyBase at the end of November 2014