2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource

Abstract

The Rat Genome Database (RGD, https://rgd.mcw.edu) has evolved from simply a resource for rat genetic markers, maps, and genes, by adding multiple genomic data types and extensive disease and phenotype annotations and developing tools to effectively mine, analyze, and visualize the available data, to empower investigators in their hypothesis-driven research. Leveraging its robust and flexible infrastructure, RGD has added data for human and eight other model organisms (mouse, 13-lined ground squirrel, chinchilla, naked mole-rat, dog, pig, African green monkey/vervet, and bonobo) besides rat to enhance its translational aspect. This article presents an overview of the database with the most recent additions to RGD's genome, variant, and quantitative phenotype data. We also briefly introduce Virtual Comparative Map (VCMap), an updated tool that explores synteny between species as an improvement to RGD's suite of tools, followed by a discussion regarding the refinements to the existing PhenoMiner tool that assists researchers in finding and comparing quantitative data across rat strains. Collectively, RGD focuses on providing a continuously improving, consistent, and high-quality data resource for researchers while advancing data reproducibility and fulfilling Findable, Accessible, Interoperable, and Reusable (FAIR) data principles.

Keywords: Rattus norvegicus; FAIR data; Rat Genome Database; comparative genome; genomics; quantitative phenotype; rat genetics; rat strain.

Fig. 1.

The Rat Genome Database JBrowse genome browser displaying a) feature density of mRatBN7.2 genes and transcripts, nervous system disease-related QTLs and strains, and feature data of the Lrrk2 gene; b) feature density of SHRSP/BbbUtx genes and transcripts; c) feature density of SHR/Utx; and d) feature density of WKY/Bbb in chromosome 7.

Fig. 2.

Using Virtual Comparative Map (VCMap) to explore the Lrrk2 gene in rat, human, and mouse; a) VCMap is found in the “Analysis & Visualization” menu on the Rat Genome Database homepage; b) using the “Load by Gene” option to explore the Lrrk2 gene by gene name; c) using the “Load by Position” to explore the Lrrk2 gene by its genomic position; d) the “Overview” section displays an overview of the gene and its syntenic region; and e) the “Detailed” section provides more detailed information of the gene and syntenic region with Slc2a13 and Abcd2 genes upstream of Lrrk2 gene.

Fig. 3.

Exploring the Lrrk2 gene and its variants in rat; a) the Rat Genome Database rat gene report page for the Lrrk2 gene linking to its variants; b) variant overview page that shows all the rat Lrrk2 gene variants; c) Variant Visualizer tool to select rat strain-specific variants; d) option to choose polyphen prediction type.

Fig. 4.

Exploring the Lrrk2 gene variants in rat using the Variant Visualizer tool; a) results page from Variant Visualizer tool displays the rat strain-specific damaging variants for the Lrrk2 gene; b) clicking on the LE/Stm rat strain opens the Variant Details display that has the “Go to Variant Page” link that; c) opens the variant report page for that variant.

Fig. 5.

Exploring the LRRK2 gene and its variants in human with a) its gene report page; b) Variant Visualizer; c) results from the Variant Visualizer showing variants from ClinVar and GWAS Catalog; d) Variant Details display and “Go to Variant Page” that; e) opens up the variant report page containing additional information.

Fig. 6.

Number of PhenoMiner records for different rat strain categories.

Fig. 7.

Exploring different rat strain measurements using PhenoMiner: a) PhenoMiner interface that shows options to select strains, clinical measurements, measurement methods, and experimental methods to “Generate Report”; b) option to edit query and download results; c) legend reflects the color represented in the graph; and d) the graph can be colored by strain, condition, phenotype, method, and sex.