Enhanced Echinobase: A Community Genome Resource for the Future

增强型 Echinobase：未来的社区基因组资源

• 批准号: 10241290
• 负责人: CHARLES A. ETTENSOHN
• 金额: $ 52.49万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-20 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10241290
• 关键词: ATAC-seq; Anatomy; Animal Model; Biological Models; Biology; Birth; ChIP-seq; Communities; Controlled Vocabulary; Custom; Data; Databases; Defect; Development; Developmental Gene; Developmental Process; EchinoBase; Echinodermata; Educational workshop; Elements; Embryonic Development; Ensure; Experimental Models; Future; Gene Expression; Genes; Genetic Variation; Genome; Genomics; Goals; Inherited; Internet; Knowledge; Lead; Letters; Link; Literature; Logic; Modeling; Ontology; Orthologous Gene; Paper; Performance; Process; Proteome; Publications; Regulator Genes; Research; Research Personnel; Research Support; Resources; Role; Scientist; Sea Urchins; Structure; Surveys; System; Systems Analysis; Taxonomy; Text; Time; Training; Untranslated RNA; Update; Vocabulary; Work; XenBase; base; cost; data integration; design; functional genomics; genome resource; genomic data; improved; network models; predictive modeling; repository; spatiotemporal; syntax; transcriptome; web app; web interface; web site; web-accessible

ENHANCED ECHINOBASE: A COMMUNITY GENOMICS RESEARCH RESOURCE FOR THE FUTURE Overall Summary Echinobase (Echinobase.org) is a database that houses all of the diverse genomic data types produced by biologists working with echinoderms. It is accessed through a website that allows scientists to search, view and download a range of datatypes to empower their own research. Echinoderms are one of only three major phyla within the deuterostomes, and therefore the species within this clade encompass a large taxonomic diversity of body plans. Species of echinoderms are powerful model systems for understanding the processes by which the genome controls development. For example, they have uniquely contributed to understanding how gene expression is regulated in time and space and how networks of interacting genes, or Gene Regulatory Networks (GRNs) control development. The proposal here will migrate current Echinobase data to a customized clone of Xenbase with underlying Chado schema. As a consequence, Echinobase will inheriting enhanced database functionality, web application capabilities, and performance upgrades, all at a fraction of the cost of doing this independently. A key added feature obtained through this work will be database modules that support curation and searches of gene expression data, and thus effort is proposed to curate gene expression data to exploit this important capability. The look and feel of Echinobase will however be unique, and be tailored to its user base. A further goal of this proposal is to develop an echinoderm embryological anatomy schema using controlled vocabularies, and to improve identification of orthologous genes, not only among echinoderms but also to common reference proteomes. These initiatives follow emerging best practices, and hence ensure that Echinobase data can be readily shared with other resources. The assembly and annotation of echinoderm genomes, including the identification of both genic and noncoding regulatory features, will also be improved. Significant improvements to the curation of these genic and nongenic elements are also proposed. The new resource will also support an interactive module to model GRNs. These enhancements are directed at providing data types to support research for which the echinoderms have known strengths and where they can contribute uniquely to reveal the mechanistic links between the genome and development. The goal is to integrate these components to allow a user to readily navigate through these different data types in the different species. Changes will also be made throughout, to make this resource more useable, e.g. by controlling vocabularies, improving website design, and by providing training and workshops, in order to increase the usefulness of the resource. The improvements suggested throughout this proposal have wide community support as evidenced by results of our survey and community White Paper, boh referenced in the component, and 34 attached letters of support. 1

增强型 ECHINOBASE：未来的社区基因组学研究资源 总体总结 Echinobase (Echinobase.org) 是一个数据库，其中包含由 研究棘皮动物的生物学家。它可以通过一个网站访问，科学家可以通过该网站搜索、查看和 下载一系列数据类型以支持自己的研究。棘皮动物是仅有的三种主要动物之一 后口动物门，因此该分支内的物种涵盖了一个大的分类学 身体计划的多样性。棘皮动物物种是理解这一过程的强大模型系统 基因组通过它控制发育。例如，他们为理解做出了独特的贡献 基因表达如何在时间和空间上受到调节，以及相互作用的基因或基因的网络如何 监管网络（GRN）控制发展。这里的提案将把当前的 Echinobase 数据迁移到 具有底层 Chado 架构的 Xenbase 的定制克隆。因此，Echinobase 将继承 增强的数据库功能、Web 应用程序功能和性能升级，所有这些都只需一小部分 独立完成这项工作的成本。通过这项工作获得的一个关键附加功能将是数据库模块 支持基因表达数据的管理和搜索，因此建议努力管理基因 表达数据来利用这一重要功能。然而，Echinobase 的外观和感觉将是独一无二的， 并根据其用户群进行定制。该提案的另一个目标是开发一种棘皮动物胚胎学 使用受控词汇的解剖图，并改进直系同源基因的识别，不仅 棘皮动物之间以及常见的参考蛋白质组。这些举措遵循新兴最佳 实践，从而确保 Echinobase 数据可以轻松地与其他资源共享。大会 棘皮动物基因组的注释和注释，包括基因和非编码调控的鉴定 功能，也将得到改进。这些基因和非基因元素的管理得到显着改进 也提出了。新资源还将支持交互式模块来对 GRN 进行建模。这些 增强功能旨在提供数据类型以支持棘皮动物已知的研究 优势以及他们可以在揭示基因组和生物之间的机制联系方面做出独特贡献 发展。目标是集成这些组件，以便用户能够轻松地浏览这些组件 不同物种的数据类型不同。整个过程中也会进行更改，以使该资源 更有用，例如通过控制词汇、改进网站设计以及提供培训和 研讨会，以提高资源的实用性。整个过程中建议的改进 正如我们的调查结果和社区白皮书所证明的那样，提案得到了社区的广泛支持， 组件中引用的 boh，以及附加的 34 封支持信。 1