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Kaldunski ML, Smith JR, Hayman GT, Brodie K, De Pons JL, Demos WM, Gibson AC, Hill ML, Hoffman MJ, Lamers L, Laulederkind SJF, Nalabolu HS, Thorat K, Thota J, Tutaj M, Tutaj MA, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research. Mamm Genome 2021; 33:66-80. [PMID: 34741192 PMCID: PMC8570235 DOI: 10.1007/s00335-021-09932-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/21/2021] [Indexed: 01/21/2023]
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.
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Affiliation(s)
- M L Kaldunski
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - J R Smith
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - G T Hayman
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - K Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - J L De Pons
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - W M Demos
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - A C Gibson
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M L Hill
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M J Hoffman
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - L Lamers
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - S J F Laulederkind
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - H S Nalabolu
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - K Thorat
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - J Thota
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M Tutaj
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M A Tutaj
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M Vedi
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - S J Wang
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - S Zacher
- Information Services, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M R Dwinell
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - A E Kwitek
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
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Horowitz BN, Kutinsky IB, Linde A. Species-Spanning Echocardiography: Cardiovascular Insights from Across the Animal Kingdom. Curr Cardiol Rep 2020; 22:165. [PMID: 33037937 DOI: 10.1007/s11886-020-01417-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
Abstract
PURPOSE OF REVIEW The objective of this review is to present comparative echocardiography as a source of insights for human cardiovascular medicine. RECENT FINDINGS We present echocardiographic examples of high impact human cardiovascular pathologies, including valvular, vascular, conduction, and myocardial disorders, in a wide range of species in varying environments. Unique features associated with comparative echocardiographic assessments are linked to human cardiology, including natural animal models of resistance and vulnerability. The cardiovascular vulnerabilities and strengths of other species can be a source of invaluable insights for human healthcare professionals. Echocardiography is playing a key role in bridging human and veterinary cardiology. Consequently, species-spanning echocardiography can deliver novel insights for human medicine.
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Affiliation(s)
- B N Horowitz
- Department of Medicine, Harvard Medical School, Boston, MA, USA. .,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. .,David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| | - Ilana B Kutinsky
- William Beaumont School of Medicine, Oakland University, Rochester, MI, USA
| | - Annika Linde
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, USA
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Smith JR, Hayman GT, Wang SJ, Laulederkind SJF, Hoffman MJ, Kaldunski ML, Tutaj M, Thota J, Nalabolu HS, Ellanki SLR, Tutaj MA, De Pons JL, Kwitek AE, Dwinell MR, Shimoyama ME. The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. Nucleic Acids Res 2020; 48:D731-D742. [PMID: 31713623 PMCID: PMC7145519 DOI: 10.1093/nar/gkz1041] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022] Open
Abstract
Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 in 2020, the Year of the Rat. Because the laboratory rat, Rattus norvegicus, has been used as a model for complex human diseases such as cardiovascular disease, diabetes, cancer, neurological disorders and arthritis, among others, for >150 years, RGD has always been disease-focused and committed to providing data and tools for researchers doing comparative genomics and translational studies. At its inception, before the sequencing of the rat genome, RGD started with only a few data types localized on genetic and radiation hybrid (RH) maps and offered only a few tools for querying and consolidating that data. Since that time, RGD has expanded to include a wealth of structured and standardized genetic, genomic, phenotypic, and disease-related data for eight species, and a suite of innovative tools for querying, analyzing and visualizing this data. This article provides an overview of recent substantial additions and improvements to RGD's data and tools that can assist researchers in finding and utilizing the data they need, whether their goal is to develop new precision models of disease or to more fully explore emerging details within a system or across multiple systems.
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Affiliation(s)
- Jennifer R Smith
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- To whom correspondence should be addressed. Tel: +1 414 955 8871; Fax: +1 414 955 6595;
| | - G Thomas Hayman
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J F Laulederkind
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Matthew J Hoffman
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Genomic Sciences and Precision Medicine Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L Kaldunski
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Harika S Nalabolu
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Santoshi L R Ellanki
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- Genomic Sciences and Precision Medicine Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- Genomic Sciences and Precision Medicine Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary E Shimoyama
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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