Enhanced Echinobase: A Community Genome Resource for the Future

增强型棘单胞菌：未来的社区基因组学研究资源 总体汇总 Echinobase（Echinobase.org）是一个数据库，其中包含所有不同的基因组数据类型， 研究棘皮动物的生物学家它是通过一个网站，允许科学家搜索，查看和 下载一系列的数据库来支持他们自己的研究。棘皮动物是世界上仅有的 门内的后口，因此，在这个分支内的物种包括一个大的分类 身体计划的多样性。棘皮动物的物种是理解这一过程的强大模型系统 基因组控制发育的机制例如，他们对理解 基因表达是如何在时间和空间上受到调节的，以及相互作用的基因网络，或基因 监管网络控制发展。这里的提议将把当前的Echinobase数据迁移到 具有底层Chado架构的Xenbase的自定义克隆。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， 独立做这件事的代价。通过这项工作获得的一个关键的新增功能将是数据库模块 其支持基因表达数据的管理和搜索，并且因此提出了管理基因表达数据的努力。 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特的， 并根据其用户群进行定制。该建议的另一个目标是开发棘皮动物胚胎学 使用受控词汇表的解剖学模式，并改善正交基因的鉴定，不仅 棘皮动物中的蛋白质组，也是常见的参考蛋白质组。这些举措遵循新兴的最佳做法， 实践，从而确保Echinobase数据可以随时与其他资源共享。大会 和棘皮动物基因组的注释，包括基因和非编码调控的鉴定 功能也将得到改善。对这些基因和非基因元素的管理进行了重大改进 也提出了。新的资源还将支持一个交互式模块来模拟GRN。这些 增强的目标是提供数据类型，以支持棘皮动物已知的研究 优势和他们可以做出独特的贡献，以揭示基因组之间的机械联系， 发展我们的目标是集成这些组件，以允许用户轻松地浏览这些组件 不同物种的不同数据类型。也将在整个过程中进行更改，以使此资源 更有用，例如通过控制词汇，改进网站设计，并通过提供培训和 研讨会，以提高资源的有用性。在整个过程中提出的改进建议 调查结果及社区白色文件显示， 该部分中提到的boh，以及34封所附的支持信。 1

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