Faculty Collaboration Database

2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource. Genetics 2023 May 04;224(1)

Date

03/18/2023

Pubmed ID

36930729

Pubmed Central ID

PMC10474928

DOI

10.1093/genetics/iyad042

Scopus ID

2-s2.0-85159551813 (requires institutional sign-in at Scopus site)   6 Citations

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.

Author List

Vedi M, Smith JR, Thomas Hayman G, Tutaj M, Brodie KC, De Pons JL, Demos WM, Gibson AC, Kaldunski ML, Lamers L, Laulederkind SJF, Thota J, Thorat K, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE

Authors

Melinda R. Dwinell PhD Professor in the Physiology department at Medical College of Wisconsin
G. Thomas Hayman PhD Research Scientist II in the Physiology department at Medical College of Wisconsin
Anne E. Kwitek PhD Professor in the Physiology department at Medical College of Wisconsin
Stanley J. Laulederkind Research Scientist II in the Physiology department at Medical College of Wisconsin
Monika Tutaj Research Scientist II in the Physiology department at Medical College of Wisconsin
Mahima Vedi Research Scientist I in the Physiology department at Medical College of Wisconsin
Shur-Jen Wang Research Scientist II in the Physiology department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Animals
Databases, Genetic
Dogs
Genome
Genomics
Humans
Mice
Oligopeptides
Reproducibility of Results
Swine