The Rat Genome Database (RGD) was established in 1999 and rapidly became the premier site for genetic, genomic, phenotype, and disease-related data generated from rat research. In addition, RGD has expanded to include a large body of structured and standardized data for ten species (rat, mouse, human, chinchilla, bonobo, 13-lined ground squirrel, dog, pig, green monkey/vervet and naked mole-rat). Much of this data is the result of manual curation work by RGD curators. In other instances, it has been imported into RGD from other databases through custom ELT (Extract, Load and Transform) pipelines giving RGD users integrated access to a wide variety of data to support their research efforts. RGD also offers a growing suite of innovative tools for querying, analyzing and visualizing this data making it a valuable resource for researchers worldwide.
RGD is deeply committed to the principles of FAIR data exchange, making data Findable, Accessible, Interoperable and Reusable. Our data is freely available for use and download. The code for our tools is available on GitHub at https://github.com/rat-genome-database. Our use of controlled vocabularies and ontologies to standardize our representation of data allows us to integrate data from diverse sources and make them both accessible and interoperable. We actively collaborate with researchers and other databases to develop and promote the use of such vocabularies and data standards in support of the FAIR principles. One illustration of RGD’s participation in the establishment and use of FAIR data standards and data exchange is FAIRsharing.org’s network diagram for RGD, seen here.
To cite RGD:
Please use the following references:
2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource.
Vedi M, Smith JR, Hayman GT, Tutaj M, Brodie KC, De Pons JL, Demos WM, Gibson AC, Kaldunski ML, Lamers L, Laulederkind SJF, Thota J, Thorat K, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. Genetics 2023. iyad042. doi: 10.3390/genes13122304.
PMID: 36930729
The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform.
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.
Nucleic Acids Res. 2019 Nov 12. pii: gkz1041. doi: 10.1093/nar/gkz1041.
PMID:31713623
RGD Species
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| Rat | Mouse | Human | Chinchilla | Bonobo | ||||
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| Dog | 13-lined Ground Squirrel |
Pig | Green Monkey |
Naked Mole-Rat |
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RGD Personnel
| Principal Investigator Anne Kwitek, PhD |
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Co-Investigator Mindy Dwinell, PhD |
| Project Manager Jennifer Smith, MSc |
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Bioinformatics Manager Jeff De Pons, BSc |
| Research Scientists and Curators Wendy Demos, MSc Tom Hayman, PhD Mary Kaldunski, BSc Stan Laulederkind, PhD Monika Tutaj, PhD Mahima Vedi, PhD Shur-Jen Wang, PhD |
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Developers Adam Gibson, BSc Logan Lamers, BSc Akhilanand Kundurthi, MSc Varun Reddy Gollapally, MSc Jyothi Thota, MSc Marek Tutaj, MSc |
| Database Administrator Stacy Zacher, MSc |
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Systems Administrator Kent Brodie, MSc |
| Scientific Advisory Board James Amos-Landgraf, Ph.D., University of Missouri Bill Hogan, M.D., M.S., University of Florida College of Medicine Sandy Martin, Ph.D., University of Colorado Denver Carolyn Mattingly, Ph.D., North Carolina State University Martin W. McBride, Ph.D., University of Glasgow Abe Palmer, Ph.D., University of California San Diego Joel Richardson, Ph.D., Jackson Laboratory Peter Robinson, M.D., MSc., Jackson Laboratory Laura Saba, Ph.D., University of Colorado Denver Jim Shull, Ph.D., University of Wisconsin Madison |
