FlyBase: a guided tour of highlighted features

Abstract

FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster. As FlyBase enters our fourth decade of service to the research community, we reflect on our unique aspects and look forward to our continued collaboration with the larger research and model organism communities. In this study, we emphasize the dedicated reports and tools we have constructed to meet the specialized needs of fly researchers but also to facilitate use by other research communities. We also highlight ways that we support the fly community, including an external resources page, help resources, and multiple avenues by which researchers can interact with FlyBase.

Keywords: Drosophila; FlyBase; model organism database.

Fig. 1.

a) The FlyBase QuickSearch tool, a collection of a dozen search tools. The “Search FlyBase” tab supports uploading a list of multiple IDs or symbols into the search. b) The “References” QuickSearch tab. In addition to searching the FlyBase bibliography, this tab includes a link to search fly preprints at Europe PMC.

Fig. 2.

The FlyBase HitList. A HitList resulting from a search for the text string “dop” has been filtered by the data class “Allele.” The filtered HitList, which includes alleles from multiple species, can now be viewed as a table, or further manipulated using the “Convert,” “Export,” or “Analyze” button menus.

Fig. 3.

a) The responsive table includes options to show, hide, or sort columns; hidden columns are displayed next to the Show/Hide Columns button. b) The responsive table shown in panel (a) has been customized, sorting the table by the “Tagged with” column (bringing tagged transgenic constructs to the top of the list), showing the previously hidden “Tag uses” column (to provide information about the nature of the tag), and hiding the “Also carries” column. c) The “GAL etc” QuickSearch HitList uses responsive tables to filter HitLists that can initially be very large. In this case, a search for transgenic reporters expressed in the mushroom body has over 5,000 hits. The list has been narrowed by filtering the “Expression terms” and “Encoded tool use(s)” columns to show only split-GAL4 drivers expressed in the gamma lobe of the mushroom body.

Fig. 4.

Main branches of the controlled vocabulary tree used to describe “Uses” of experimental tools. Term report for experimental tool descriptor (FBcv: 0005001) with children set to a hierarchy level of 1.

Fig. 5.

High-throughput data displayed in JBrowse. This view shows DGRP variant data, and two sets of transcription start sites.

Fig. 6.

a) TopoView. This view shows stranded RNA-seq data, in the default view using a log2 signal scale and a tilted, tightly spaced display. Each colored track represents a specific developmental time point, tissue, and/or sex from which samples were collected. b) Customizable TopoView display options. This view shows the same data as in panel (a) displayed using a linear signal scale. c) This view displays the same data using a log2 signal scale with increased vertical spacing, making it easier to see the tracks at the rear.