Rat Genome Database

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。随着数据集的数量、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地使用它们。RGD的目标是以单一、全面、高效的资源服务于社区。为了实现这一目标，我们提出了以下具体目标： 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。区域数据司将维护数据并将其分发到主要数据库。 2.整理基因组序列草案。保持草稿顺序是一个独特的挑战。与贝勒大学合作，我们将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排序的区域，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参考大鼠基因。 3.增加RGD的生物含量。研究基因组对更高层次生理学的影响。最初的重点是增加大鼠品系的注释，它们的生物学措施，以及跨多个物种的QTL。我们将通过本体注释扩展生物学内容，捕获基因功能变体和途径注释的数据，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的优势，并将随着人类和小鼠功能数据的增加而扩展。随着序列的验证，我们将比较图从基于RH数据转换为基于序列。我们将使用表型和疾病本体来比较菌株和物种之间的生理数据。利用比较作图的分析工具将有助于填补序列，并提高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区域指导数据的活动将继续进行，并辅之以在线培训，新的教育门户利用多媒体演示、扩大的词汇表、教程和案例研究。一个访问科学家计划将支持专业生物数据集的管理、分析和整合。

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.