Enhanced Echinobase: A Community Genome Resource for the Future

增强型ECHINOBASE：面向未来的社区基因组研究资源 总体摘要 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，该网站允许科学家搜索、查看和 下载一系列数据类型以支持他们自己的研究。棘皮动物是仅有的三种主要动物之一 后口动物中的门，因此这一支系中的物种包含了一个很大的分类学 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式系统 基因组通过它来控制发育。例如，它们对理解 基因表达是如何在时间和空间上被调控的，以及相互作用的基因网络是如何 监管网络(GRN)控制发展。这里的建议将把当前的Echinbase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，全部成本仅为 独立完成这项工作的成本。通过这项工作获得的一个关键新增功能将是数据库模块 支持基因表达数据的管理和搜索，因此建议对基因进行管理 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， 并为其用户群量身定做。这项提议的另一个目标是开发棘皮动物胚胎 使用受控词汇的解剖图式，并改进对同源基因的识别，不仅 棘皮动物之间，也有共同的参考蛋白质组。这些举措紧跟着新兴的最佳做法 因此，确保Echinobase数据可以随时与其他资源共享。该组件 和棘皮动物基因组的注释，包括识别基因和非编码调控 功能，也将得到改进。对这些基因和非基因元件的管理有重大改进 也提出了一些建议。新资源还将支持一个互动模块，以模拟GRN。这些 增强的目的是提供数据类型以支持棘皮动物已知的研究 优势以及它们可以在哪里做出独特贡献，以揭示基因组和基因组之间的机械联系 发展。目标是集成这些组件，使用户能够轻松地在这些组件中导航 不同物种中的不同数据类型。还将在整个过程中进行更改，以使此资源 更易用，例如通过控制词汇表、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。在整个过程中建议的改进 我们的调查结果和社区白皮书证明，这项建议得到了广泛的社区支持， 组件中引用的BOH，以及所附的34封支持信。 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