RESUMO
The Rat Genome Database (RGD) (http://rgd.mcw.edu) aims to meet the needs of its community by providing genetic and genomic infrastructure while also annotating the strengths of rat research: biochemistry, nutrition, pharmacology and physiology. Here, we report on RGD's development towards creating a phenome database. Recent developments can be categorized into three groups. (i) Improved data collection and integration to match increased volume and biological scope of research. (ii) Knowledge representation augmented by the implementation of a new ontology and annotation system. (iii) The addition of quantitative trait loci data, from rat, mouse and human to our advanced comparative genomics tools, as well as the creation of new, and enhancement of existing, tools to enable users to efficiently browse and survey research data. The emphasis is on helping researchers find genes responsible for disease through the use of rat models. These improvements, combined with the genomic sequence of the rat, have led to a successful year at RGD with over two million page accesses that represent an over 4-fold increase in a year. Future plans call for increased annotation of biological information on the rat elucidated through its use as a model for human pathobiology. The continued development of toolsets will facilitate integration of these data into the context of rat genomic sequence, as well as allow comparisons of biological and genomic data with the human genomic sequence and of an increasing number of organisms.
Assuntos
Bases de Dados de Ácidos Nucleicos , Genômica , Fenótipo , Ratos/genética , Animais , Mapeamento Cromossômico , Sistemas de Gerenciamento de Base de Dados , Modelos Animais de Doenças , Marcadores Genéticos , Genoma , Locos de Características Quantitativas , Ratos/fisiologia , Integração de SistemasRESUMO
The broad goal of physiological genomics research is to link genes to their functions using appropriate experimental and computational techniques. Modern genomics experiments enable the generation of vast quantities of data, and interpretation of this data requires the integration of information derived from many diverse sources. Computational biology and bioinformatics offer the ability to manage and channel this information torrent. The Rat Genome Database (RGD; http://rgd.mcw.edu) has developed computational tools and strategies specifically supporting the goal of linking genes to their functional roles in rat and, using comparative genomics, to human and mouse. We present an overview of the database with a focus on these unique computational tools and describe strategies for the use of these resources in the area of physiological genomics.
Assuntos
Bases de Dados Genéticas , Genoma/genética , Genômica/métodos , Ratos/genética , Ratos/fisiologia , Animais , Clonagem Molecular , Perfilação da Expressão GênicaRESUMO
The laboratory rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have direct relevance to human-based research. The Rat Genome Database (RGD, http://rgd.mcw.edu) is a model-organism database that provides access to wide variety of curated rat data such as genes and their homologs, quantitative trait loci, phenotypes, comparative mapping, and genome analysis. We present an overview of the database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the rat. We show how to make associations with the genome and use comparative tools to link the rat with human and mouse in order to integrate results from these three species of critical biomedical importance.