FlyBase December 2016
- 1 1. Staff working on GOC tasks
- 2 2. Annotation progress
- 3 3. Methods and strategies for annotation
- 4 4. Presentations and publications
- 5 5. Other Highlights:
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_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 2014 - Nov 2015 (FB2014_06 - FB2015_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)
- 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.