Mining Information from Echinoderm Genomes and the Scientific Literature

即审即审 棘皮动物基因组和科学文献中的信息挖掘 棘皮动物(海胆及其同源动物)是分析海胆的基因组控制的有价值的模型。 胚胎发育。例如，最完整的发育基因调控网络(GRN) 我们对任何动物的研究最近都解决了海胆胚胎的问题。跨区域比较研究 棘皮动物正在阐明基因调控程序的进化。关于基因、基因组和基因的数据 表达是现代发育生物学研究的各个方面的基础。有效访问 这些数据不仅对棘皮动物研究界的成员至关重要，而且对更广泛的 研究许多模型系统中的发展过程的观众。棘球藻酶的活性为 为了最终将这些科学信息应用于人类发展和疾病，这是至关重要的。 模型生物数据库通过整合和存储数据、集成 不同类型的信息，并以有用的方式表示它，并将类似类型的数据链接到 有机体。棘球虫数据库的创建是为了提高与基因和基因组相关的科学数据的价值 作为有关海胆和其他棘皮动物的一个集中、权威的资源 这些重要的模式生物。策展部分(策展)在整个过程中起着核心作用。 棘球虫数据库的任务是识别、提取和组织科学数据。我们所有的管理工作都是 通过与Xenbase的密切协作提供支持，Xenbase提供一套数据输入、存储和 非常适合我们需要的分析工具。 在这个项目期间，CURATE有三个主要目标：1)管理棘皮动物基因组，包括 为棘皮动物基因提供准确的、基于正字法的名称，并改进当前的注释 棘皮动物基因模型；2)整理与棘皮动物发育相关的大量科学文献， 包括正在进行的已发表论文的书目汇编，这是所有 精选的生物数据归因于，从这些论文中精选出的大量信息与 基因表达模式、吗啡、抗体、引导RNA(GRNAs)和顺式调节元件(Cres)； 3)增强现有棘皮动物发育本体论，为几乎所有 我们的管理工作，通过扩展本体论以包括其他类别的棘皮动物的代表 和附加的生命历史阶段，并通过将派生自以下内容的附加静态内容合并到Echinobase 发展本体论。通过实现这些目标，CURATE将极大地增强Echinobase的效用 研究棘皮动物发育并确保与棘皮动物相关的研究人员社区 研究包括脊椎动物在内的其他模式生物的生物学家可以很容易地获取信息。

SUMMARY CURATION Mining Information from Echinoderm Genomes and the Scientific Literature Echinoderms (sea urchins and their allies) are valuable models for analysis of the genomic control of embryonic development. For example, the most complete gene regulatory networks (GRNs) for development that we have for any animal have recently been solved for sea urchin embryos. Comparative studies across echinoderms are elucidating the evolution of gene regulatory programs. Data on genes, genomes, and gene expression are fundamental to all aspects of modern developmental biological research. Effective access to these data has become vital not only to members of the echinoderm research community but to a broader audience studying developmental processes in many model systems. The activities of Echinobase are essential in order to ultimately apply this scientific information to human development and disease. Model organism databases enhance the value of research by consolidating and storing data, integrating different types of information and representing it in useful ways, and linking similar kinds of data across organisms. Echinobase was created to enhance the value of scientific data related to the genes and genomes of sea urchins and other echinoderms and to serve as a centralized, definitive resource for information related to these important model organisms. The Curate Component (Curate) plays a central role in the overall mission of Echinobase by identifying, extracting, and organizing scientific data. All of our curation efforts are supported through a close collaboration with Xenbase, which provides a suite of data entry, storage, and analysis tools that are well-suited to our needs. During this project period, Curate has three major goals: 1) to curate echinoderm genomes, including the provision of accurate, orthology-based names to echinoderm genes and the improved annotation of current echinoderm gene models; 2) to curate an extensive scientific literature related to echinoderm development, including the ongoing assembly of a bibliography of published papers that serves as a backbone to which all curated biological data are attributed, and the curation of a wealth of information from these papers related to gene expression patterns, morpholinos, antibodies, guide RNAs (gRNAs), and cis-regulatory elements (CREs); 3) to enhance the current echinoderm developmental ontology, which provides a foundation for almost all of our curation efforts, by expanding the ontology to include representatives of additional classes of echinoderms and additional life history stages and by incorporating into Echinobase additional static content derived from the developmental ontology. By achieving these goals, Curate will vastly enhance the utility of Echinobase to the community of researchers who study echinoderm development and ensure that echinoderm-related information is readily accessible to biologists who work with other model organisms, including vertebrates.