Rat Genome Database

大鼠基因组数据库

• 批准号: 7496592
• 负责人: HOWARD J JACOB
• 金额: $ 174.13万
• 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 2010-02-07
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7496592
• 关键词: Adopted; Alternative Splicing; Animal Model; Area; Base Sequence; Biological; Boxing; Case Study; Chromosome Mapping; Collaborations; Collection; Communities; Complex; DNA Resequencing; Daily; Data; Data Collection; Data Set; Data Storage and Retrieval; Databases; Disease; Education; Ensure; Expressed Sequence Tags; Fostering; Genbank; Gene Expression; Genes; Genetic; Genetic Markers; Genome; Genomics; Glossary; Goals; Grant; Haplotypes; Human; Length; Maintenance; Maps; Measures; Medicine; Mind; Modeling; Modification; Multimedia; Mus; Nomenclature; Numbers; Online Systems; Ontology; Organism; Pathway interactions; Physiological; Physiological Processes; Physiology; Proteomics; QTL Genes; RGD (sequence); Rat Strains; Rattus; Reporting; Research; Research Personnel; Resources; Role; Scientist; Sequence Analysis; Site; SwissProt; Training; Universities; Variant; Visit; Work; analytical tool; base; clinically relevant; college; comparative; disease phenotype; distributed data; feeding; genome database; genome sequencing; improved; programs; rat genome; repaired; size; tool; trait

DESCRIPTION (provided by applicant): Rat research was revolutionized by the draft genomic sequence. To meet the changing needs, the Rat Genome Database is expanding its focus from genomics to disease and phenotype annotation as well as genome sequence maintenance. As datasets increase in number, size and complexity we must develop web-based tools for their efficient use. The goal of RGD is to serve the community with a single, comprehensive, efficient resource. To meet this goal we propose these specific aims: 1. To Expand the Collection of Rat Genomic Data. RGD leads in annotating and integrating rat genomic data. Annotation will include all known and predicted genes; all SNPs; select haplotypes; and select gene expression and proteomics data. RGD will maintain and distribute the data to the major databases. 2. To Curate the Draft Genomic Sequence. Maintaining the draft sequence is a unique challenge. Collaborating with Baylor University, we will track and annotate sequence modifications between sequence rebuilds. RGD will maintain and improve this resource by identifying regions needing resequencing, ensuring the repair is correct, and passing the data to the major databases. We will create and maintain a reference set of rat genes. 3. To Increase the Biological Content of RGD. The genome is studied for its impact on higher-level physiology. Initially focused on increasing annotation of rat strains, their biological measures, and QTLs across multiple species. We will expand biological content through ontology annotations, capturing data on gene functional variants and pathway annotation, add physiological data to our strain reports, and enable users to compare traits between different strains. 4. To Expand Comparative Analysis Tools. Comparative genomics is a strength of RGD and will expand as functional data increases in human and mouse. As sequence is validated, we will convert comparative maps from RH data based to sequence based. We will use phenotype and disease ontology to compare physiological data between strains and species. Analysis tools utilizing comparative mapping will help fill in sequence and enhance our ability to define gene models. 5. To Provide User Education, Interaction, and Collaboration Programs. Activities promoting RGD in genetic and genomic data storage, analysis, and exploration will continue and be supplemented with online training with a new educational portal utilizing multimedia presentations, an expanded glossary, tutorials, and case studies. A visiting scientist program will support curation, analyses and integration of specialized biological datasets.

描述（由申请人提供）：基因组序列草案彻底改变了大鼠研究。为了满足不断变化的需求，大鼠基因组数据库正在将其重点从基因组学扩展到疾病和表型注释以及基因组序列维护。随着数据集数量、规模和复杂性的增加，我们必须开发基于网络的工具来有效利用它们。 RGD 的目标是以单一、全面、高效的资源为社区服务。为了实现这一目标，我们提出以下具体目标： 1. 扩大大鼠基因组数据的收集。 RGD 在注释和整合大鼠基因组数据方面处于领先地位。注释将包括所有已知和预测的基因；所有 SNP；选择单倍型；并选择基因表达和蛋白质组学数据。 RGD 将维护数据并将其分发到主要数据库。 2. 策划基因组序列草案。维持草稿顺序是一个独特的挑战。我们将与贝勒大学合作，跟踪和注释序列重建之间的序列修改。 RGD 将通过识别需要重新测序的区域、确保修复正确并将数据传递到主要数据库来维护和改进此资源。我们将创建并维护一组大鼠基因参考集。 3.增加RGD的生物含量。研究基因组对高级生理学的影响。最初专注于增加多个物种的大鼠品系、其生物学测量和 QTL 的注释。我们将通过本体注释来扩展生物学内容，捕获基因功能变异和通路注释的数据，将生理数据添加到我们的菌株报告中，并使用户能够比较不同菌株之间的性状。 4.扩展比较分析工具。比较基因组学是 RGD 的强项，并将随着人类和小鼠功能数据的增加而扩展。当序列得到验证后，我们会将基于 RH 数据的比较图转换为基于序列的图。我们将使用表型和疾病本体论来比较菌株和物种之间的生理数据。利用比较图谱的分析工具将有助于填充序列并增强我们定义基因模型的能力。 5. 提供用户教育、互动和协作计划。在遗传和基因组数据存储、分析和探索方面促进 RGD 的活动将继续进行，并辅以在线培训，其中包括利用多媒体演示、扩展术语表、教程和案例研究的新教育门户。访问科学家计划将支持专业生物数据集的整理、分析和整合。