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.

总结策展 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）是分析海胆基因组控制的宝贵模型。 胚胎发育。例如，最完整的发育基因调控网络（GRN） 我们最近已经解决了对海胆胚胎的任何动物的问题。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，而且对更广泛的领域也至关重要。 观众研究许多模型系统中的发育过程。 Echinobase 的活动是 对于最终将这些科学信息应用于人类发展和疾病至关重要。 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，并将类似类型的数据链接起来 有机体。 Echinobase 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 海胆和其他棘皮动物的信息，并作为相关信息的集中、权威的资源 这些重要的模式生物。 Curate 组件（Curate）在整体中起着核心作用 Echinobase 的使命是识别、提取和组织科学数据。我们所有的策展努力都是 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 非常适合我们需求的分析工具。 在此项目期间，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、基于直系学的名称，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， 包括正在收集已发表论文的参考书目，作为所有研究的支柱 整理的生物数据被归因，并且从这些论文中整理出与以下相关的大量信息 基因表达模式、吗啉代、抗体、引导RNA (gRNA) 和顺式调控元件(CRE)； 3）增强当前棘皮动物发育本体论，这为几乎所有的 我们的管理工作，通过扩大本体论来包括其他棘皮动物类别的代表 和额外的生命史阶段，并通过将来自 Echinobase 的额外静态内容纳入其中 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 研究棘皮动物发育并确保与棘皮动物相关的研究人员群体 研究其他模式生物（包括脊椎动物）的生物学家很容易获得信息。