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The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. Nucleic Acids Res 2015 Jan;43(Database issue):D743-50 PMID: 25355511 PMCID: PMC4383884

Pubmed ID

25355511

Abstract

The Rat Genome Database (RGD, http://rgd.mcw.edu) provides the most comprehensive data repository and informatics platform related to the laboratory rat, one of the most important model organisms for disease studies. RGD maintains and updates datasets for genomic elements such as genes, transcripts and increasingly in recent years, sequence variations, as well as map positions for multiple assemblies and sequence information. Functional annotations for genomic elements are curated from published literature, submitted by researchers and integrated from other public resources. Complementing the genomic data catalogs are those associated with phenotypes and disease, including strains, QTL and experimental phenotype measurements across hundreds of strains. Data are submitted by researchers, acquired through bulk data pipelines or curated from published literature. Innovative software tools provide users with an integrated platform to query, mine, display and analyze valuable genomic and phenomic datasets for discovery and enhancement of their own research. This update highlights recent developments that reflect an increasing focus on: (i) genomic variation, (ii) phenotypes and diseases, (iii) data related to the environment and experimental conditions and (iv) datasets and software tools that allow the user to explore and analyze the interactions among these and their impact on disease.

Author List

Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H

Authors

Melinda R. Dwinell PhD Center Associate Director, Associate Professor in the Physiology department at Medical College of Wisconsin
Mary E. Shimoyama PhD Associate Professor in the Biomedical Engineering department at Medical College of Wisconsin




Scopus

2-s2.0-84941092929   90 Citations

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

Animals
Databases, Genetic
Disease
Environment
Genetic Variation
Genome
Genomics
Internet
Molecular Sequence Annotation
Phenotype
Rats
jenkins-FCD Prod-299 9ef562391eceb2b8f95265c767fbba1ce5a52fd6