The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease
Top Cited Papers
Open Access
- 29 October 2014
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 43 (D1), D743-D750
- https://doi.org/10.1093/nar/gku1026
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.This publication has 28 references indexed in Scilit:
- The Rat Genome Database 2013--data, tools and usersBriefings in Bioinformatics, 2013
- Analysis of disease-associated objects at the Rat Genome DatabaseDatabase: The Journal of Biological Databases and Curation, 2013
- PhenoMiner: quantitative phenotype curation at the rat genome databaseDatabase: The Journal of Biological Databases and Curation, 2013
- The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013Nucleic Acids Research, 2012
- Gene Ontology Annotations and ResourcesNucleic Acids Research, 2012
- The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping dataMammalian Genome, 2012
- MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics DatabaseDatabase: The Journal of Biological Databases and Curation, 2012
- Ontology searching and browsing at the Rat Genome DatabaseDatabase: The Journal of Biological Databases and Curation, 2012
- A map of human genome variation from population-scale sequencingNature, 2010
- The Genetic Association DatabaseNature Genetics, 2004