The genome sequence of the Norway rat, Berkenhout 1769.

We present a genome assembly from an individual male (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span.

Automated generation of gene summaries at the Alliance of Genome Resources.

Short paragraphs that describe gene function, referred to as gene summaries, are valued by users of biological knowledgebases for the ease with which they convey key aspects of gene function. Manual curation of gene summaries, while desirable, is difficult for knowledgebases to sustain. We developed an algorithm that uses curated, structured gene data at the Alliance of Genome Resources (Alliance; www.

The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform.

Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 in 2020, the Year of the Rat.

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources.

As more digital resources are produced by the research community, it is becoming increasingly important to harmonize and organize them for synergistic utilization. The findable, accessible, interoperable, and reusable (FAIR) guiding principles have prompted many stakeholders to consider strategies for tackling this challenge. The FAIRshake toolkit was developed to enable the establishment of community-driven FAIR metrics and rubrics paired with manual and automated FAIR assessments.

Rat Genome Databases, Repositories, and Tools.

Resources for rat researchers are extensive, including strain repositories and databases all around the world. The Rat Genome Database (RGD) serves as the primary rat data repository, providing both manual and computationally collected data from other databases.

Predicting instances of pathway ontology classes for pathway integration.

Background: To improve the outcomes of biological pathway analysis, a better way of integrating pathway data is needed. Ontologies can be used to organize data from disparate sources, and we leverage the Pathway Ontology as a unifying ontology for organizing pathway data. We aim to associate pathway instances from different databases to the appropriate class in the Pathway Ontology.

Quantitative phenotype analysis to identify, validate and compare rat disease models.

The laboratory rat has been widely used as an animal model in biomedical research. There are many strains exhibiting a wide variety of phenotypes. Capturing these phenotypes in a centralized database provides researchers with an easy method for choosing the appropriate strains for their studies.

Integrated curation and data mining for disease and phenotype models at the Rat Genome Database.

Rats have been used as research models in biomedical research for over 150 years. These disease models arise from naturally occurring mutations, selective breeding and, more recently, genome manipulation. Through the innovation of genome-editing technologies, genome-modified rats provide precision models of disease by disrupting or complementing targeted genes.

A Primer for the Rat Genome Database (RGD).

The laboratory rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have relevance to human physiology and disease. The Rat Genome Database (RGD, http://rgd.mcw.

Disease Ontology: improving and unifying disease annotations across species.

Model organisms are vital to uncovering the mechanisms of human disease and developing new therapeutic tools. Researchers collecting and integrating relevant model organism and/or human data often apply disparate terminologies (vocabularies and ontologies), making comparisons and inferences difficult. A unified disease ontology is required that connects data annotated using diverse disease terminologies, and in which the terminology relationships are continuously maintained.

Genetics and Genomics in Clinical Practice: The Views of Wisconsin Physicians.

Introduction: Decreasing costs and increased availability of genetic testing and genome sequencing mean many physicians will consider using these services over the next few years. Despite this promising future, some argue the present roadmap for translating genetics and genomics into routine clinical practice is unclear.

Objective: We conducted a pilot study to explore Wisconsin physicians' views, practices and educational desires regarding genetic and genomic testing.

Rat Genome and Model Resources.

Rats remain a major model for studying disease mechanisms and discovery, validation, and testing of new compounds to improve human health. The rat's value continues to grow as indicated by the more than 1.4 million publications (second to human) at PubMed documenting important discoveries using this model.

Successful Application of Whole Genome Sequencing in a Medical Genetics Clinic.

A pilot program was initiated using whole genome sequencing (WGS) to diagnose suspected genetic disorders in the Genetics Clinic at Children's Hospital of Wisconsin. Twenty-two patients underwent WGS between 2010 and 2013. Initially, we obtained a 14% (3/22) diagnosis rate over 2 years; with subsequent reanalysis, this increased to 36% (8/22).

Exploring human disease using the Rat Genome Database.

Rattus norvegicus, the laboratory rat, has been a crucial model for studies of the environmental and genetic factors associated with human diseases for over 150 years. It is the primary model organism for toxicology and pharmacology studies, and has features that make it the model of choice in many complex-disease studies. Since 1999, the Rat Genome Database (RGD; http://rgd.

Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass.

Understanding the pathogenesis of disease is instrumental in delineating its progression mechanisms and for envisioning ways to counteract it. In the process, animal models represent invaluable tools for identifying disease-related loci and their genetic components. Amongst them, the laboratory rat is used extensively in the study of many conditions and disorders.

Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.

Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data.

The Chinchilla Research Resource Database: resource for an otolaryngology disease model.

The long-tailed chinchilla (Chinchilla lanigera) is an established animal model for diseases of the inner and middle ear, among others. In particular, chinchilla is commonly used to study diseases involving viral and bacterial pathogens and polymicrobial infections of the upper respiratory tract and the ear, such as otitis media. The value of the chinchilla as a model for human diseases prompted the sequencing of its genome in 2012 and the more recent development of the Chinchilla Research Resource Database (http://crrd.

The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.

The Rat Genome Database (RGD;http://rgd.mcw.edu/) provides critical datasets and software tools to a diverse community of rat and non-rat researchers worldwide.

2015 Guidelines for Establishing Genetically Modified Rat Models for Cardiovascular Research.

The rat has long been a key physiological model for cardiovascular research, most of the inbred strains having been previously selected for susceptibility or resistance to various cardiovascular diseases (CVD). These CVD rat models offer a physiologically relevant background on which candidates of human CVD can be tested in a more clinically translatable experimental setting. However, a diverse toolbox for genetically modifying the rat genome to test molecular mechanisms has only recently become available.

EHR-based phenome wide association study in pancreatic cancer.

Background: Pancreatic cancer is one of the most common causes of cancer-related deaths in the United States, it is difficult to detect early and typically has a very poor prognosis. We present a novel method of large-scale clinical hypothesis generation based on phenome wide association study performed using Electronic Health Records (EHR) in a pancreatic cancer cohort.

Methods: The study population consisted of 1,154 patients diagnosed with malignant neoplasm of pancreas seen at The Froedtert & The Medical College of Wisconsin academic medical center between the years 2004 and 2013.

PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease.

Rats have been used extensively as animal models to study physiological and pathological processes involved in human diseases. Numerous rat strains have been selectively bred for certain biological traits related to specific medical interests. Recently, the Rat Genome Database (http://rgd.

OntoMate: a text-mining tool aiding curation at the Rat Genome Database.

The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data. Converting data from free text in the scientific literature to a structured format is one of the main tasks of all model organism databases. RGD spends considerable effort manually curating gene, Quantitative Trait Locus (QTL) and strain information.

Next generation phenotyping using the unified medical language system.

Background: Structured information within patient medical records represents a largely untapped treasure trove of research data. In the United States, privacy issues notwithstanding, this has recently become more accessible thanks to the increasing adoption of electronic health records (EHR) and health care data standards fueled by the Meaningful Use legislation. The other side of the coin is that it is now becoming increasingly more difficult to navigate the profusion of many disparate clinical terminology standards, which often span millions of concepts.