Sp Base: A Sea Urchin Genome Database

Sp Base：海胆基因组数据库

• 批准号: 7488489
• 负责人: Robert Andrew Cameron
• 金额: $ 34.08万
• 依托单位: CALIFORNIA INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-01 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7488489
• 关键词: Archives; Biological; Collaborations; Communities; Computer software; Data; Databases; Developmental Biology; Elements; Embryo; Future; Gene Expression; Genes; Genome; Genomics; Goals; Home environment; Housing; Human; Institution; Internet; Left; Link; Links List; Manuals; Medicine; Modeling; Names; Publications; Publishing; Reporting; Research; Science; Sea Urchins; Site; Staging; Structure; System; Time; Update; Urination; Work; base; college; data mining; genome database; genome sequencing; member; model organisms databases; open source; research study

DESCRIPTION (provided by applicant): The overall goal of the proposed project is to extend and expand a unique genome data base for sea urchins. The database will be a modest organization incorporating relevant data produced by sea urchin research labs into the annotations and gene models emerging from the work of the Sea Urchin Genome Sequencing Project as managed by the Baylor College of Medicine, Human Genome Sequencing Center and pursued by the members of the Sea Urchin Genome Annotation team. It is specifically intended to fill the void left when the primary annotation is finished and other existing databases are not able to incorporate gene expression data and other specific biological information that can be linked to the genome sequence and gene models. The immediate utility of these data is evidenced by the publication of about 40 research reports in Developmental Biology and Science which emerged from the annotation. One of these reports describes a whole-genome tiling-array that was used to annotate and extend the predicted gene models. In addition the work reported in these publications covers extensive manual gene annotations, another microarray experiment and a wide variety of temporal and spatial gene expression determinations from embryonic stages. It is expected the linkages between much of this experimental data and the primary genomic sequences will be lost or severely degraded over time without the inception of a new database. The new sea urchin genome data base, SpBase will accumulate and maintain the genome sequence, gene annotation and ancillary biological information in a structure suitable for extensive editing, updating and installing of additional features that are specifically useful to the experimentalist using the sea urchin system. The task will be efficiently accomplished through a collaboration that gives us access to software modules from GMOD and expertise from the Wormbase project, a model organism database housed at our home institution.

描述（由申请人提供）：拟议项目的总体目标是扩展和扩展一个独特的海胆基因组数据库。该数据库将是一个适度的组织，将海胆研究实验室产生的相关数据整合到海胆基因组测序项目的注释和基因模型中，该项目由贝勒医学院人类基因组测序中心管理，并由海胆基因组注释团队的成员进行研究。它专门用于填补初级注释完成后，其他现有数据库无法纳入基因表达数据和其他可链接到基因组序列和基因模型的特定生物信息时留下的空白。这些数据的直接效用由《发育生物学与科学》上发表的大约40篇研究报告证明，这些报告来自该注释。其中一份报告描述了一个全基因组平铺阵列，用于注释和扩展预测的基因模型。此外，这些出版物中报道的工作涵盖了大量的手工基因注释，另一个微阵列实验和胚胎阶段各种各样的时间和空间基因表达测定。如果不建立新的数据库，预计许多实验数据和主要基因组序列之间的联系将随着时间的推移而丢失或严重退化。新的海胆基因组数据库SpBase将积累和维护基因组序列、基因注释和辅助生物信息，其结构适合于广泛的编辑、更新和安装额外的功能，这些功能对使用海胆系统的实验人员特别有用。这项任务将通过合作有效地完成，该合作使我们能够访问GMOD的软件模块和来自Wormbase项目的专业知识，这是一个位于我们国内机构的模式生物数据库。