Using FlyBase, a Database of Drosophila Genes and Genomes
For nearly 25 years, FlyBase (flybase.org) has provided a freely available online database of biological information about Drosophila species, focusing on the model organism D. melanogaster. The need for a centralized, integrated view of Drosophila research has never been greater as advances in genomic, proteomic, and high-throughput technologies add to the quantity and diversity of available data and resources.
FlyBase has taken several approaches to respond to these changes in the research landscape. Novel report pages have been generated for new reagent types and physical interaction data; Drosophila models of human disease are now represented and showcased in dedicated Human Disease Model Reports; other integrated reports have been established that bring together related genes, datasets, or reagents; Gene Reports have been revised to improve access to new data types and to highlight functional data; links to external sites have been organized and expanded; and new tools have been developed to display and interrogate all these data, including improved batch processing and bulk file availability. In addition, several new community initiatives have served to enhance interactions between researchers and FlyBase, resulting in direct user contributions and improved feedback.
This chapter provides an overview of the data content, organization, and available tools within FlyBase, focusing on recent improvements. We hope it serves as a guide for our diverse user base, enabling efficient and effective exploration of the database and thereby accelerating research discoveries.
Key wordsFlyBase Drosophila Database Genetics Genomics Translational research
FlyBase is funded by the National Human Genome Research Institute at the U.S. National Institutes of Health (#U41HG000739, PI W.M. Gelbart) and the U.K. Medical Research Council (#G1000968, PI N.H. Brown). Support is also provided by the Indiana Genomics Initiative and the National Science Foundation through XSEDE resources provided by Indiana University. At the time of writing, the FlyBase Consortium included William Gelbart, Norbert Perrimon, Cassandra Extavour, Kris Broll, Madeline Crosby, Gilberto dos Santos, David Emmert, Sian Gramates, Kathleen Falls, Beverley Matthews, Susan Russo Gelbart, Andrew Schroeder, Christopher Tabone, Pinglei Zhou, Mark Zytkovicz; Nicholas Brown, Giulia Antonazzo, Helen Attrill, Marta Costa, Steven Marygold, Gillian Millburn, Laura Ponting, Alix Rey, Nicole Staudt, Raymund Stefancsik, Jose-Maria Urbano; Thomas Kaufman, Josh Goodman, Gary Grumbling, Victor Strelets, Jim Thurmond; Richard Cripps, Maggie Werner-Washburne, Phillip Baker.
DedicationWe wish to mark the passing of our colleague and one of FlyBase’s founders, Dr. William Gelbart, who continued in his role of PI until his death. Bill’s leadership, enthusiasm, insight and humor will be greatly missed.
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