The Rat Genome Database (RGD) is a database of rat genomics, genetics, physiology and functional data, as well as data for comparative genomics between rat, human and mouse. RGD is responsible for attaching biological information to the rat genome via structured vocabulary, or ontology, annotations assigned to genes and quantitative trait loci (QTL), and for consolidating rat strain data and making it available to the research community. They are also developing a suite of tools for mining and analyzing genomic, physiologic and functional data for the rat, and comparative data for rat, mouse, human, and five other species. RGD began as a collaborative effort between research institutions involved in rat genetic and genomic research. Its goal, as stated in the National Institutes of Health’s Request for Grant Application: HL-99-013, is the establishment of a Rat Genome Database to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make this data widely available to the scientific community. A secondary, but critical goal is to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data. The rat continues to be extensively used by researchers as a model organism for investigating pharmacology, toxicology, general physiology and the biology and pathophysiology of disease. In recent years, there has been a rapid increase in rat genetic and genomic data. In addition to this, the Rat Genome Database has become a central point for information on the rat for research and now features information on not just genetics and genomics, but physiology and molecular biology as well. There are tools and data pages available for all of these fields that are curated by RGD staff.

Data

RGD’s data consists of manual annotations from RGD researchers as well as imported annotations from a variety of different sources. RGD also exports their own annotations to share with others. RGD's Data page lists eight types of data stored in the database: Genes, QTLs, Markers, Maps, Strains, Ontologies, Sequences and References. Of these, six are actively used and regularly updated. The RGD Maps datatype refers to legacy genetic and radiation hybrid maps. This data has been largely supplanted by the rat whole genome sequence. The Sequences data type is not a full list of either genomic, transcript or protein sequences, but rather mostly contains PCR primer sequences which define simple sequence length polymorphism (SSLP) and expressed sequence tag (EST) Markers. Such sequences are useful primarily for researchers still using these markers for genotyping their animals and for distinguishing between markers of the same name. The six major data types in RGD are as follows:

Genome tools

RGD's Genome tools include both software tools developed at RGD and tools from third party sources.

Genome tools developed at RGD

RGD develops web-based tools designed to use the data stored in the RGD database for analyses in rat and across species. These include:

Third party genome tools adapted for use with RGD data

RGD offers several third party software tools that have been adapted for use on the website utilizing data stored in the RGD database. These include:

Additional Data and Tools

Phenotypes and Models Portal

RGD's Phenotypes and Models portal focuses on strains, phenotypes and the rat as a model organism for physiology and disease.

Disease Portals

Disease Portals consolidate the data in RGD for a specific disease category and present it in a single group of pages. Genes, QTLs and strains annotated to any disease in the category are listed, with genome-wide views of their locations in rat, human and mouse (see Genome Viewer in Genome tools developed at RGD). Additional sections of the portal display data for phenotypes, biological processes and pathways related to the disease category. Pages are also supplied to give users access to information about rat strains used as models for one or more diseases in the category, tools that could be used to analyze the data and additional resources related to the disease category. Further, access to the RGD's Multi-Ontology Enrichment Tool (MOET) is available at the bottom of the individual disease portals. As of May 2021, RGD has fifteen disease portals: Disease portals consolidate the data in RGD for a specific disease category and present it in a single group of pages. Genes, QTLs and strains annotated to any disease in the category are listed, with genome-wide views of their locations in rat, human and mouse (see "Genome Viewer" in Genome tools developed at RGD). Additional sections of the portal display data for phenotypes, biological processes and pathways related to the disease category. Pages are also supplied to give users access to information about rat strains used as models for one or more diseases in the category, tools that could be used to analyze the data and additional resources related to the disease category.

Pathways

RGD's Pathway resources include a Pathway Ontology of pathway terms (developed and maintained at RGD, encompassing not only metabolic pathways but also disease, drug, regulatory and signaling pathways), as well as interactive diagrams of the components and interactions of selected pathways. Included on the diagram pages are a description, lists of pathway gene members and additional elements, tables of disease, pathway and phenotype annotations made to pathway member genes, associated references and an ontology path diagram. Pathway Suites and Suite Networks, i.e. groupings of related pathways which all contribute to a larger process such as glucose homeostasis or gene expression regulation are presented, as well as Physiological Pathway diagrams which display networks of organs, tissues, cells and molecular pathways at the whole animal or systems level.

Knockouts

Until recently, direct, specific genomic manipulations in the rat were not possible. However, with the rise of technologies such as Zinc finger nuclease- and CRISPR -based mutagenesis techniques, that is no longer the case. Groups producing rat gene knockouts and other types of genetically modified rats include the Human and Molecular Genetics Center at MCW. RGD links to information about the rat strains produced in these studies via pages about the PhysGen Knockout project and the MCW Gene Editing Rat Resource Center (GERRC), accessed from RGD page headers. Funding for both the PhysGenKO project and the GERRC came from the National Heart Lung and Blood Institute (NHLBI). The stated goal of both projects is to produce rats with alterations in one or more specific genes related to the mission of the NHLBI. Genes were nominated by rat researchers. Nominations were adjudicated by an External Advisory Board. In the case of the PhysGenKO project, many of the rats produced by the group were phenotyped using a standardized high-throughput phenotyping protocol and the data is available in RGD's PhenoMiner tool.

Community outreach and education

RGD reaches out to the rat research community in a variety of ways including an email forum, a news page, a Facebook page, a Twitter account, and regular attendance and presentations at scientific meetings and conferences. Additional educational activities include the production of tutorial videos, both outlining how to use RGD tools and data, and on more general topics such as biomedical ontologies and biological (i.e. gene, QTL and strain) nomenclature. These videos can be viewed on several online video hosting sites including YouTube.

Funding

RGD is funded by grant R01HL64541 from the National Heart, Lung, and Blood Institute (NHLBI) on behalf of the National Institutes of Health (NIH). The principal investigator of the grant is Anne E. Kwitek, who was appointed to this leadership position from Mary E. Shimoyama, in March 2020. Melinda R Dwinell is Co-Investigator.

New Genome Assembly

The new genome rat assembly, mRatBN7.2, was generated by the Darwin Tree of Life Project at the Wellcome Sanger Institute and has been accepted into the Genome Reference Consortium. mRatBN7.2 was derived from a male BN/NHsdMcwi rat that is a direct descendant of the female BN rat previously sequenced. The new BN rat reference genome was created using a variety of technologies including PacBio long reads, 10X linked reads, Bionano maps and Arima Hi-C. Its contiguity is similar to the human or mouse reference assemblies. It is available at NCBI’s GenBank and at RefSeq, and it will be made the primary assembly at RGD in the near future.