The goal of the Rat Genome Database (RGD) is to provide a research platform encompassing comprehensive genetic, genomic, physiological, and phenotype datasets, and innovative software tools for data mining, presentation and analysis. RGD's user community includes those using rat to investigate genomic elements involved in biological and disease processes, clinical researchers using rat models to understand the impact of genetic and environmental variations on disease and those using informatics and computational approaches to analyze data. To support this diverse user group, we will 1) acquire and integrate genomic elements including variations and regulatory units along with mapped phenotype data, 2) enhance this catalogue with functional, disease, and phenotype annotations for genomic elements, comprehensive phenotype profiles for strains and curated molecular, drug, and disease pathways, and 3) create a research platform of innovative software tool systems to mine, display, integrate, and analyze both public and user datasets to promote discovery. Recognizing the comparative nature of much of the research conducted by our community, RGD will continue to provide comparative genomic tools including rat, human and mouse genome browsers, interactive pathway diagrams for multiple organisms and analysis tools leveraging functional data from rat, human and mouse. As part of our quality control process we will assign official nomenclature for genomic elements, QTL and rat strains. To ensure a robust platform and to provide support for the informatics community we will continue to follow industry best practices in database and software development and provide Web Services and REST API, expanded FTP site and integration of batch query tools such as Ratmine. RGD will continue to support users of multiple browsers and develop platforms for multiple devices including mobile.

Public Health Relevance

The rat has been a primary animal model used to study many complex diseases and physiological processes. The combination of available genomic resources and wealth of phenotypic data that exists for the rat provides an opportunity to advance the understanding of disease processes and develop new diagnostic, preventative and treatment approaches. However, the large and often disparate data sets are difficult to mine and analyze. The primary goal of RGD is to reduce the complex data sets, and large volume of literature into a discovery platform that provides support for researchers using the rat as a model organism in which to understand human health and disease through disease-oriented translational research.

Agency
National Institute of Health (NIH)
Institute
National Heart, Lung, and Blood Institute (NHLBI)
Type
Research Project (R01)
Project #
5R01HL064541-18
Application #
9197669
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Luo, James
Project Start
1999-09-30
Project End
2018-12-31
Budget Start
2017-01-01
Budget End
2017-12-31
Support Year
18
Fiscal Year
2017
Total Cost
Indirect Cost
Name
Medical College of Wisconsin
Department
Surgery
Type
Schools of Medicine
DUNS #
937639060
City
Milwaukee
State
WI
Country
United States
Zip Code
53226
Shimoyama, Mary; Smith, Jennifer R; Bryda, Elizabeth et al. (2017) Rat Genome and Model Resources. ILAR J 58:42-58
Petri, Victoria; Hayman, G Thomas; Tutaj, Marek et al. (2016) Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass. Comput Struct Biotechnol J 14:35-48
Wang, Shur-Jen; Laulederkind, Stanley J F; Hayman, G Thomas et al. (2016) Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database. Physiol Genomics 48:589-600
Huntley, Rachael P; Sitnikov, Dmitry; Orlic-Milacic, Marija et al. (2016) Guidelines for the functional annotation of microRNAs using the Gene Ontology. RNA 22:667-76
Shimoyama, Mary; Laulederkind, Stanley J F; De Pons, Jeff et al. (2016) Exploring human disease using the Rat Genome Database. Dis Model Mech 9:1089-1095
Hayman, G Thomas; Laulederkind, Stanley J F; Smith, Jennifer R et al. (2016) The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database. Database (Oxford) 2016:
Liu, Weisong; Laulederkind, Stanley J F; Hayman, G Thomas et al. (2015) OntoMate: a text-mining tool aiding curation at the Rat Genome Database. Database (Oxford) 2015:
Shimoyama, Mary; De Pons, Jeff; Hayman, G Thomas et al. (2015) The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. Nucleic Acids Res 43:D743-50
Wang, Shur-Jen; Laulederkind, Stanley J F; Hayman, G Thomas et al. (2015) PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease. Database (Oxford) 2015:
Gene Ontology Consortium (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res 43:D1049-56

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