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Review
. 2019 Jan 8;47(D1):D759-D765.
doi: 10.1093/nar/gky1003.

FlyBase 2.0: the next generation

Collaborators, Affiliations
Review

FlyBase 2.0: the next generation

Jim Thurmond et al. Nucleic Acids Res. .

Abstract

FlyBase (flybase.org) is a knowledge base that supports the community of researchers that use the fruit fly, Drosophila melanogaster, as a model organism. The FlyBase team curates and organizes a diverse array of genetic, molecular, genomic, and developmental information about Drosophila. At the beginning of 2018, 'FlyBase 2.0' was released with a significantly improved user interface and new tools. Among these important changes are a new organization of search results into interactive lists or tables (hitlists), enhanced reference lists, and new protein domain graphics. An important new data class called 'experimental tools' consolidates information on useful fly strains and other resources related to a specific gene, which significantly enhances the ability of the Drosophila researcher to design and carry out experiments. With the release of FlyBase 2.0, there has also been a restructuring of backend architecture and a continued development of application programming interfaces (APIs) for programmatic access to FlyBase data. In this review, we describe these major new features and functionalities of the FlyBase 2.0 site and how they support the use of Drosophila as a model organism for biological discovery and translational research.

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Figures

Figure 1.
Figure 1.
GAL4 Search Result. A result table for a search using the ‘GAL4 etc’ QuickSearch tab, with the ‘integrated table’ output option selected. Cross-references are used to group associated alleles, constructs, insertions and stocks together. Two ‘frequently-used’ GAL4 drivers are flagged.
Figure 2.
Figure 2.
Search Result Hitlist. The result page for Search FlyBase using ‘Mad’ as the search term. A ‘hitlist’ is displayed containing genes, stocks, alleles, and many other classes of FlyBase data items (some not shown). The Mad gene report button is marked with a blue flag, indicating new annotations in the current release; mousing over the flag shows a summary. The list is framed with an array of tools for filtering by data class and species, pagination, view and analysis.
Figure 3.
Figure 3.
Table View of Search Result Hitlist. The ‘Mad’ search result page, filtered to the Allele data class and toggled to table view. The Export tool menu has been expanded.
Figure 4.
Figure 4.
FlyBase Gene Report. FlyBase Gene Report for the Cdk1 gene. The General Information section serves as a ‘super-summary’ of gene information. The ‘Report Sections’ menu at right floats as the user scrolls in the report, providing an easy navigation tool. The Genomic Location section includes external links to genome browsers at NCBI, Ensembl, UCSC and PopFly.
Figure 5.
Figure 5.
GO Summary Ribbon. GO summary ribbon for D. melanogaster gene Cdk1, as embedded in a FlyBase Gene Report.
Figure 6.
Figure 6.
Interactive References Section. References section with options for filtering by publication types (left sidebar) including representative publications, and various sort, search, and export options.

References

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