Published online 21 November 2020 Nucleic Acids Research, 2021, Vol. 49, Database issue D899–D907 doi: 10.1093/nar/gkaa1026 FlyBase: updates to the Drosophila melanogaster knowledge base Aoife Larkin 1,*, Steven J. Marygold 1, Giulia Antonazzo1, Helen Attrill 1, Gilberto dos Santos2, Phani V. Garapati1, Joshua L. Goodman3,L.SianGramates 2, Gillian Millburn1, Victor B. Strelets3, Christopher J. Tabone2, Jim Thurmond3 and FlyBase Consortium†
1
Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge Downloaded from https://academic.oup.com/nar/article/49/D1/D899/5997437 by guest on 15 January 2021 CB2 3DY, UK, 2The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA and 3Department of Biology, Indiana University, Bloomington, IN 47405, USA
Received September 15, 2020; Revised October 13, 2020; Editorial Decision October 14, 2020; Accepted October 22, 2020
ABSTRACT In this paper, we highlight a variety of new features and improvements that have been integrated into FlyBase since FlyBase (flybase.org) is an essential online database our last review (3). We have introduced a number of new fea- for researchers using Drosophila melanogaster as a tures that allow users to more easily find and use the data in model organism, facilitating access to a diverse ar- which they are interested; these include customizable tables, ray of information that includes genetic, molecular, improved searching using expanded Experimental Tool Re- genomic and reagent resources. Here, we describe ports, more links to and from other resources, and bet- the introduction of several new features at FlyBase, ter provision of precomputed bulk files. We have upgraded including Pathway Reports, paralog information, dis- tools such as Fast-Track Your Paper and ID validator. We ease models based on orthology, customizable ta- have also introduced more high-level groupings to improve bles within reports and overview displays (‘ribbons’) data accessibility; these include our curated Pathway Re- of expression and disease data. We also describe a ports that facilitate understanding and exploration of a number of major signaling pathways, as well as new sum- variety of recent important updates, including incor- mary ‘ribbons’ representing expression and disease model poration of a developmental proteome, upgrades to data. In order to further promote and simplify user-led in- the GAL4 search tab, additional Experimental Tool vestigation of genes, we have integrated new paralog infor- Reports, migration to JBrowse for genome browsing mation, reviewed and revised functional data for enzymes and improvements to batch queries/downloads and and introduced a novel orthology-based pipeline to iden- the Fast-Track Your Paper tool. tify D. melanogaster genes potentially relevant to human disease. Finally, we give details about our genome browser change from GBrowse to JBrowse (4). INTRODUCTION FlyBase (flybase.org) is the leading database and web por- tal for data related to the fruit fly, Drosophila melanogaster. IMPROVEMENTS FOR ACCESSING AND SORTING FlyBase contains a wide variety of data types curated from REAGENTS published scientific literature and incorporated from other New responsive tables databases, and strives to continually improve display and functionality for users. Gene Report pages have a number We have introduced responsive tables into our reports, al- of sections that may be of interest to the user; where ap- lowing users to customize the display and easily access the plicable, these include: genomic information, Gene Ontol- subset of the data that is important to them. These tables ogy (GO, 1) annotations, transcripts, protein domains, ex- are currently implemented in the ‘Alleles, Insertions, and pression, alleles and transgenic constructs, phenotypes, or- Transgenic Constructs’ of Gene Reports, the ‘Members’ thologs, human disease models, physical and genetic inter- section of Pathway Reports and the hitlist of results of the actions, stocks and reagents, and associated references. New QuickSearch GAL4 etc. tab (Figure 1). We plan to expand users of FlyBase may find it useful to refer to Marygold et them to other tables on the website. Key features include al (2). the ability to Show/Hide columns, column reordering, row
*To whom correspondence should be addressed. Tel: +44 1223333865; Email: [email protected] †The members of the FlyBase Consortium are listed in the Acknowledgements.