FlyBase: updates to the Drosophila melanogaster knowledge base

Abstract

FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays ('ribbons') of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool.

Figure 1.

Responsive tables can be filtered, sorted and rearranged by users to easily browse or search genetic reagents. FlyBase has incorporated responsive tables into (A) the ‘Alleles, Insertions and Transgenic Constructs’ section of Gene Reports, (B) the ‘GAL4 etc’ QuickSearch hitlist and (C) the Frequently Used GAL4 Drivers table.

Figure 2.

(A) The ‘Hedgehog Signaling Pathway’ page includes a description of the pathway, links to sub-groups and other related gene groups. The interactive Physical Interaction Network contains pathway gene members as nodes and physical interactions form the edges between them. The node size for each gene increases in the range 1–10 supporting papers, with no increase beyond 10, showing the relative experimental data for each gene's inclusion. (B) The members table for the Hedgehog Signaling Pathway Core Components is shown, with columns ordered by the number of references with curated supporting experimental data. (C) Gene Reports now feature a ‘Pathways’ section, which includes links to FlyBase Pathway pages and other pathway resources.

Figure 3.

Disease model summary ribbon and ‘potential disease model’ annotations for Fmr1. The subsection showing potential disease models (based on orthology to human genes associated with disease ‘disease genes’), indicates that Drosophila melanogaster Fmr1 may model three different diseases based on orthology to human FMR1. These computed disease model annotations are combined with experimental annotations (included within the closed section in this screenshot) to populate the disease summary ribbon.

Figure 4.

(A) Paralogs section of the Drosophila melanogaster RpS28a report, showing that two other genes (RpS28b and RpS28-like) are identified as paralogs by the indicated sources. A link is provided to ‘Download all DIOPT Paralogs’, which is useful if many paralogs are listed. (B) Paralogs can be searched using the ‘Homologs’ tab of the QuickSearch tool by selecting ‘D. melanogaster’ as both the input and output species.

Figure 5.

ID Validator input form (A) and output page (B). Submitted items that have been updated from their original values are highlighted with a pale yellow background. In cases where a single submitted item is now represented by two or more validated IDs, an exclamation mark ‘!’ is appended to the value in the ‘Submitted Item’ column.