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.

摘要策划 来自棘皮动物基因组和科学文献的采矿信息 棘皮动物（海胆及其盟友）是分析基因组控制的宝贵模型 胚胎发展。例如，用于开发的最完整的基因调节网络（GRN） 我们最近为海胆胚胎解决了任何动物。跨越比较研究 棘皮动物正在阐明基因调节程序的演变。基因，基因组和基因的数据 表达是现代发展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 在许多模型系统中研究发展过程的受众。 echinobase的活动是 为了最终将这些科学信息应用于人类发展和疾病，至关重要的。 模拟生物数据库通过合并和存储数据，集成来增强研究的价值 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 有机体。创建了棘皮动物酶是为了增强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，并作为与信息相关的集中式，确定的资源 这些重要的模型生物。策展人组件（策展人）在整体中起着核心作用 通过识别，提取和组织科学数据来使Echinobase的任务。我们所有的策划都是 通过与Xenbase的密切合作支持，该XENBase提供了一套数据输入，存储和 非常适合我们需求的分析工具。 在这个项目期间，策展人有三个主要目标：1）策划棘皮动物基因组，包括 提供基于棘皮动物基因的准确的，基于矫正的名称，并改善了当前的注释 棘皮动物基因模型； 2）策划与棘皮动物发展有关的广泛科学文献， 包括正在进行 策划的生物学数据归因于这些论文的大量信息的策划与 基因表达模式，形态学，抗体，引导RNA（GRNA）和顺式调节元件（CRES）； 3）增强当前的棘皮动物发育本体，这为几乎所有的所有 我们的策划工作，扩大本体论以包括其他类似类胚层的代表 以及其他生活历史阶段，并通过将echinobase纳入额外的静态内容。 发展本体论。通过实现这些目标，Curate将极大地增强Echinobase的实用性 研究棘皮动物开发并确保与棘皮动物相关的研究人员社区 与其他模型生物（包括脊椎动物）合作的生物学家可以轻松访问信息。