Abstract
Model organism research is essential for discovering the mechanisms of human diseases by defining biologically meaningful gene to disease relationships. The Rat Genome Database (RGD, (https://rgd.mcw.edu)) is a cross-species knowledgebase and the premier online resource for rat genetic and physiologic data. This rich resource is enhanced by the inclusion and integration of comparative data for human and mouse, as well as other human disease models including chinchilla, dog, bonobo, pig, 13-lined ground squirrel, green monkey, and naked mole-rat. Functional information has been added to records via the assignment of annotations based on sequence similarity to human, rat, and mouse genes. RGD has also imported well-supported cross-species data from external resources. To enable use of these data, RGD has developed a robust infrastructure of standardized ontologies, data formats, and disease- and species-centric portals, complemented with a suite of innovative tools for discovery and analysis. Using examples of single-gene and polygenic human diseases, we illustrate how data from multiple species can help to identify or confirm a gene as involved in a disease and to identify model organisms that can be studied to understand the pathophysiology of a gene or pathway. The ultimate aim of this report is to demonstrate the utility of RGD not only as the core resource for the rat research community but also as a source of bioinformatic tools to support a wider audience, empowering the search for appropriate models for human afflictions.
Highlights
A major challenge for preclinical research is finding, or establishing, a good model for the human disease of interest—one that best recapitulates the phenotypic and genomic profile of that disease in the human system
Recognizing that the best model system to study human disease depends on the disease etiology and the specific research question, the wide-ranging bioinformatics platform for rat at Rat Genome Database (RGD) is enhanced by integration of other mammalian species’ genomic and phenotypic data, human, making it ideally suited for facilitating translational research at a single point of access
The laboratory rat has been used as a model to study human disease for over 160 years
Summary
A major challenge for preclinical research is finding, or establishing, a good model for the human disease of interest—one that best recapitulates the phenotypic and genomic profile of that disease in the human system. Many animal models are studied to understand human biology and disease. Integrating multidimensional data from multiple species may aid in understanding human disease. RGD (https://www.rgd.mcw.edu, (Smith et al 2020)) is recognized as a comprehensive data resource for laboratory rat (Rattus norvegicus) as a model for the study of human disease (Laulederkind et al 2019). Recognizing that the best model system to study human disease depends on the disease etiology and the specific research question, the wide-ranging bioinformatics platform for rat at RGD is enhanced by integration of other mammalian species’ genomic and phenotypic data, human, making it ideally suited for facilitating translational research at a single point of access. RGD has been the front-runner in this endeavor, even before the first public
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