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: 10442594
• 负责人: CHARLES A. ETTENSOHN
• 金额: $ 53.83万
• 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 2023-09-21
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10442594
• 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; 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; gene regulatory network; 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

增强的Echinobase：一种社区基因组学研究资源 总结 echinobase（echinobase.org）是一个数据库，它包含由由 生物学家使用棘皮动物。它可以通过网站访问，该网站允许科学家搜索，查看和 下载一系列数据型以增强自己的研究。棘皮动物是仅有的三个主要 氘代表内的门，因此该进化枝中的物种涵盖了大型分类学 身体计划的多样性。棘皮动物的物种是理解过程的强大模型系统 基因组控制发展。例如，他们为理解做出了独特的贡献 如何在时间和空间中调节基因表达，以及相互作用基因或基因的网络如何调节 监管网络（GRNS）控制开发。这里的建议将迁移当前的echinobase数据到 Xenbase的定制克隆，带有基础Chado模式。结果，echinobase将继承 增强数据库功能，Web应用程序功能和性能升级，均以一小部分 独立执行此操作的成本。通过这项工作获得的关键添加功能将是数据库模块 支持策划和搜索基因表达数据，因此提出了努力来策划基因 表达数据以利用这一重要功能。但是 并根据其用户群量身定制。该提案的另一个目标是开发棘皮动物的胚胎学 使用受控词汇的解剖模式，并改善直系同源基因的识别，不仅 在棘皮动物中，也是常见的参考蛋白质组。这些举措遵循新兴 实践，因此确保可以轻松地与其他资源共享echinobase数据。大会 棘皮动物基因组的注释，包括鉴定遗传和非编码调节 功能也将得到改善。这些基因和非元素元件的策展的显着改善 也提出了。新资源还将支持一个交互模块来建模GRN。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 优势及其在哪里可以为揭示基因组和 发展。目的是集成这些组件，以允许用户轻松浏览这些组件 不同物种中的不同数据类型。也将在整个过程中进行更改，以制造此资源 更可用的，例如通过控制词汇，改进网站设计以及提供培训和 讲习班，以增加资源的有用性。在整个过程中提出的改进 我们的调查结果和社区白皮书的结果证明了建议的广泛社区支持， 组件中引用的boh和34个附带的支持字母。 1