Mining Information from Echinoderm Genomes and the Scientific Literature

从棘皮动物基因组和科学文献中挖掘信息

• 批准号: 10715580
• 负责人: CHARLES A. ETTENSOHN
• 金额: $ 14.94万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-22 至 2028-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10715580
• 关键词: Ally; Animals; Antibodies; Architecture; Bibliography; Biological; Biological Models; Biology; Collaborations; Communities; Comparative Study; Data; Databases; Development; Developmental Process; EchinoBase; Echinodermata; Embryo; Embryonic Development; Ensure; Evolution; FAIR principles; Foundations; Future; Gene Expression; Gene Expression Profile; Genes; Genetic Transcription; Genome; Genomics; Goals; Grant; Guide RNA; Heart; Human Development; Individual; Link; Literature; Mining; Mission; Modeling; Modernization; Names; Ontology; Organism; Paper; Play; Publications; Publishing; Reagent; Regulator Genes; Regulatory Element; Research; Research Personnel; Resources; Role; Sea Urchins; Time; Tissues; Vertebral column; Vertebrates; Work; XenBase; biological research; data management; gene regulatory network; human disease; improved; journal article; life history; member; model organism; model organisms databases; programs; scientific organization; tool

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.

总结治疗 从棘皮动物基因组和科学文献中挖掘信息 棘皮动物（海胆及其盟友）是分析基因组控制的有价值的模型， 胚胎发育例如，最完整的基因调控网络（GRNs） 我们对任何动物的研究最近在海胆胚胎上得到了解决。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。有效获得 这些数据不仅对棘皮动物研究界的成员至关重要， 观众在许多模型系统中学习发展过程。Echinobase的活性是 为了最终将这些科学信息应用于人类发展和疾病，这是必不可少的。 模式生物数据库通过整合和存储数据，整合 不同类型的信息，并以有用的方式表示它，并将类似的数据链接到 有机体创建Echinobase是为了提高与基因和基因组相关的科学数据的价值 海胆和其他棘皮动物的信息，并作为一个集中的，明确的资源， 这些重要的模式生物。Curate组件（Curate）在整体中发挥着核心作用 通过识别、提取和组织科学数据，完成Echinobase的使命。我们所有的策展工作 通过与Xenbase的密切合作提供支持，Xenbase提供了一套数据输入、存储和 这些分析工具非常适合我们的需求。 在这个项目期间，Curate有三个主要目标：1）策划棘皮动物基因组，包括 为棘皮动物基因提供准确的、基于直系同源的名称， 棘皮动物基因模型; 2）收集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，作为所有 策展的生物学数据归因，以及从这些论文中收集的大量信息， 基因表达模式、吗啉代、抗体、向导RNA（gRNA）和顺式调节元件（CREs）; 3)加强目前的棘皮动物发育本体，这为几乎所有的 我们的策展工作，通过扩大本体，包括其他类别的棘皮动物的代表， 和额外的生活史阶段，并通过将来自以下的额外静态内容并入Echinobase 发展本体论通过实现这些目标，Curate将大大提高Echinobase的实用性， 研究棘皮动物发育并确保棘皮动物相关 研究包括脊椎动物在内的其他模式生物的生物学家很容易获得信息。