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

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, t...

Full description

Saved in:
Bibliographic Details
Published in:Genetics (Austin) Vol. 224; no. 1
Main Authors: Vedi, Mahima, Smith, Jennifer R, Thomas Hayman, G, Tutaj, Monika, Brodie, Kent C, De Pons, Jeffrey L, Demos, Wendy M, Gibson, Adam C, Kaldunski, Mary L, Lamers, Logan, Laulederkind, Stanley J F, Thota, Jyothi, Thorat, Ketaki, Tutaj, Marek A, Wang, Shur-Jen, Zacher, Stacy, Dwinell, Melinda R, Kwitek, Anne E
Format: Journal Article
Language:English
Published: United States 04.05.2023
Subjects:
Animals
Chlorocebus aethiops
Databases, Genetic
Dogs
Genome
Genomics
Humans
Mice
Oligopeptides
Reproducibility of Results
Swine
rat genetics
quantitative phenotype
Rattus norvegicus
rat strain
genomics
FAIR data
Rat Genome Database
comparative genome
ISSN:1943-2631, 1943-2631
Online Access:Get more information
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1943-2631
1943-2631
DOI:10.1093/genetics/iyad042