Rat Genome Database

大鼠基因组数据库

• 批准号: 8021847
• 负责人: HOWARD J JACOB
• 金额: $ 185.02万
• 依托单位: MEDICAL COLLEGE OF WISCONSIN
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-09-30 至 2014-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8021847
• 关键词: Animal Model; Biological; Biological Process; Biology; Breeding; Chemicals; Collaborations; Communities; Comparative Study; Complex; Data; Data Set; Databases; Development; Disease; Disease Pathway; Disease model; Drug Interactions; Educational Activities; Elements; Environment; Equilibrium; Gene Mutation; Genes; Genetic; Genetic Models; Genetic Variation; Genome; Genomics; Genotype; Goals; Grant; Health; Human; Human Genome; Imagery; Individual; Knowledge; Link; Literature; Mammalian Genetics; Maps; Measurement; Medical Records; Methods; Mining; Modeling; Molecular; Mus; Nature; Ontology; Pathway interactions; Pharmaceutical Preparations; Phenotype; Physiological; Physiological Processes; Positioning Attribute; Process; Protocols documentation; Quantitative Trait Loci; RNA Splicing; Rat Strains; Rattus; Regulatory Pathway; Reporting; Reproduction; Research; Research Personnel; Resources; Signal Pathway; Single Nucleotide Polymorphism; Site; Software Tools; System; Translational Research; Variant; computerized data processing; data format; disease phenotype; editorial; embryonic stem cell; gene interaction; genetic variant; genome database; human disease; innovation; interest; meetings; mouse genome; novel diagnostics; phenome; public health relevance; rat genome; tool; tool development

DESCRIPTION (provided by applicant): The Rat Genome Database provides a core resource for rat researchers combining genetic, genomic, pathway, phenotype and strain information with a focus on disease. The goal of RGD is to provide investigators with a research platform that facilitates the elucidation of disease mechanisms by implementing standard data formats and ontologies. To meet this goal, we propose three specific aims: 1) To acquire, integrate and functionally annotate emerging genomic elements and variations along with core data to create a comprehensive genome resource. New gene models, sequence and map data and variations such as single nucleotide polymorphisms (SNPs), copy number variants (CNVs), and splice variants will be integrated through collaborations with NCBI and Ensembl and the use of innovative data pipelines. Curators will continue to focus on functional annotation of core data using multiple ontologies. New information including chemical-gene, drug-gene interactions and their impact on biology or disease will be added. Tools will be developed for mining, analysis and visualization of new data types. Educational activities for this aim will focus on new users and new tools for existing users. 2) To create a comprehensive phenome resource including phenotype measurements and strain medical records. We will develop a phenome database and provide individual strain "medical records" to provide easy access to the richness of this information. The phenome resource will include specific educational activities focused on phenotyping protocols, breeding and the use of our new tools and strain resources. 3) To link genotypes (Aim 1) to phenotypes (Aim 2) through QTLs, molecular, cellular and physiological pathways and the disease portals. RGD will continue to curate QTL data and enhance the QTL reports to provide a navigational hub linking genotype and phenotype data. Drug and physiological pathways will be curated in addition to disease related signaling and regulatory pathways and interactive diagrams will be used to link pathways, biological processes, genomic variations and phenotype data. RGD will expand its Disease Portals to serve as integration points for genomic and phenotype data, disease model profiles, and pathway data. Educational activities will focus on tools for comparative studies between rat and human, as well as those which integrate genotype and phenotype data. PUBLIC HEALTH RELEVANCE: The rat has been a primary animal model used to study many complex diseases and physiological processes. The combination of available genomic resources with the biological relevance and wealth of phenotypic data that exists for the rat provides an opportunity to advance the understanding of disease processes and develop new diagnostic, preventative and treatment approaches. However, the large and often disparate data sets are difficult to gain knowledge from. The primary goal of RGD is to reduce the complex data sets, and large volume of literature into a discovery platform that provides support for researchers using the rat as a model organism in which to understand human health and disease through disease-oriented translational research.

描述(由申请人提供)：大鼠基因组数据库为大鼠研究人员提供了一个核心资源，将遗传、基因组、途径、表型和菌株信息与重点放在疾病上。RGD的目标是为研究人员提供一个研究平台，通过实施标准的数据格式和本体来促进疾病机制的阐明。为了实现这一目标，我们提出了三个具体目标：1)获取、整合和在功能上注释新出现的基因组元件和变异以及核心数据，以创建一个全面的基因组资源。新的基因模型、序列和地图数据以及变异，如单核苷酸多态(SNPs)、拷贝数变异(CNV)和剪接变异，将通过与NCBI和EnSembl的合作以及创新数据管道的使用来整合。馆长将继续专注于使用多个本体对核心数据进行功能性注释。将增加新的信息，包括化学-基因、药物-基因相互作用及其对生物学或疾病的影响。将开发新数据类型的挖掘、分析和可视化工具。为此目的开展的教育活动将侧重于新用户和现有用户的新工具。2)建立包括表型测定和品系病历在内的综合表型资源。我们将开发一个表型数据库，并提供个体品系“病历”，以方便获取丰富的信息。表型组资源将包括特定的教育活动，重点是表型鉴定协议、育种以及我们新工具和菌株资源的使用。3)通过QTL、分子、细胞和生理途径以及疾病门户，将基因类型(目标1)与表型(目标2)联系起来。RGD将继续整理QTL数据并增强QTL报告，以提供一个连接基因和表型数据的导航枢纽。除了疾病相关的信号和调节途径外，还将对药物和生理途径进行管理，并将使用互动图将途径、生物过程、基因组变异和表型数据联系起来。RGD将扩大其疾病门户网站，作为基因组和表型数据、疾病模型概况和途径数据的集成点。教育活动将侧重于老鼠和人类之间的比较研究工具，以及那些整合了基因和表型数据的工具。 公共卫生相关性：大鼠一直是研究许多复杂疾病和生理过程的主要动物模型。现有的基因组资源与大鼠现有的生物学相关性和丰富的表型数据相结合，为促进对疾病过程的理解和开发新的诊断、预防和治疗方法提供了机会。然而，很难从庞大且往往完全不同的数据集中获取知识。RGD的主要目标是将复杂的数据集和大量文献减少到一个发现平台，为研究人员使用大鼠作为模式生物通过面向疾病的翻译研究了解人类健康和疾病提供支持。