Mining the Scientific Literature and Building a Pan-Echinoderm Gene Expression Database

挖掘科学文献并构建泛棘皮动物基因表达数据库

• 批准号: 10442596
• 负责人: CHARLES A. ETTENSOHN
• 金额: $ 11.37万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-20 至 2023-09-21
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10442596
• 关键词: Ally; Anatomy; Animal Model; Animals; Antibodies; Bacterial Artificial Chromosomes; Bibliography; Biological; Biological Models; Biology; Cell Lineage; Collaborations; Communities; Controlled Vocabulary; Data; Data Store; Development; Developmental Biology; Developmental Process; Dominant-Negative Mutation; EchinoBase; Echinodermata; Embryo; Embryonic Development; Formulation; Future; Gene Expression; Gene Expression Profile; Genes; Genome; Genomics; Goals; Heart; Human Development; In Situ Hybridization; Individual; Link; Literature; Manuals; Mining; Mission; Modeling; Modernization; Names; Ontology; Organism; Paper; Pathway Analysis; Pattern; Plasmids; Play; Publications; Publishing; Reporter; Research; Research Personnel; Resources; Role; Scientist; Sea Urchins; System; Taxonomy; Time; Update; Vertebral column; Work; XenBase; annotation system; base; comparative; flexibility; gene expression database; gene regulatory network; genome resource; human disease; improved; interest; journal article; mRNA Expression; member; model organisms databases; nano-string; novel; protein expression; tool; transcriptome sequencing; user-friendly

CURATION COMPONENT- ABSTRACT Echinoderms (sea urchins and their allies) are a pre-eminent model 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. Data on genes, genomes, and gene expression are fundamental to all aspects of modern developmental biology, including GRN biology. 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 (including GRNs) in other 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. During this project period, Curate has two overarching goals: 1) the curation of scientific literature related to echinoderm development, and 2) the development of a comprehensive gene expression database, including the formulation of an anatomical ontology for echinoderm embryos that will serve as a framework for the annotation of gene expression data. Literature curation will allow users to effectively mine information from the large body of published studies on echinoderm development, and the bibliography of published papers will serve as a backbone to which all curated biological data can be attributed. Among the most important classes of biological data are those pertaining to spatial and temporal patterns of gene expression during development. A wealth of gene expression data has been generated for sea urchins and other echinoderms in recent years, and there is a pressing need to curate these data and to develop new tools that will allow scientists to take full advantage of this information. Our curation efforts will be supported through a collaboration with Xenbase, which will provide a suite of data entry, storage, and analysis tools that are well-suited to our needs. Through its activities, Curate will extend the capabilities of Echinobase and thereby greatly enhance its utility to the research community.

策展部分-摘要 棘皮动物（海胆及其盟友）是分析基因组控制的杰出模型 胚胎发育的情况。例如，最完整的基因调控网络（GRN） 我们对任何动物的发育最近已经在海胆胚胎上得到解决。基因数据， 基因组和基因表达是现代发育生物学各个方面的基础，包括 GRN 生物学。有效获取这些数据不仅对棘皮动物研究人员至关重要 社区，但面向更广泛的受众，研究其他模型中的发育过程（包括 GRN） 系统。 Echinobase 的活动对于最终将这些科学信息应用于 人类发展与疾病。 模式生物数据库通过整合和存储数据来提高研究价值， 整合不同类型的信息并以有用的方式表示它，并链接相似类型的数据 跨生物体。 Echinobase 的创建是为了提高与基因和基因相关的科学数据的价值。 海胆和其他棘皮动物的基因组，并作为集中的、权威的资源 与这些重要模式生物相关的信息。 Curate 组件（Curate）发挥着核心作用 通过识别、提取和组织科学数据来完成 Echinobase 的总体使命。 在此项目期间，Curate 有两个总体目标：1）科学文献的策展 与棘皮动物发育相关，以及2）开发综合基因表达数据库， 包括制定棘皮动物胚胎的解剖本体，该本体将作为框架 基因表达数据的注释。文献策展将允许用户有效地挖掘信息 关于棘皮动物发育的大量已发表研究以及已发表论文的参考书目将 作为所有精选生物数据的支柱。最重要的课程之一 生物数据是与发育过程中基因表达的空间和时间模式有关的数据。 近年来，海胆和其他棘皮动物产生了大量的基因表达数据， 迫切需要整理这些数据并开发新工具，使科学家能够充分利用 利用这些信息。我们的管理工作将通过与 Xenbase 的合作得到支持， 它将提供一套非常适合我们需求的数据输入、存储和分析工具。通过 Curate 将扩展 Echinobase 的功能，从而大大增强其对 研究社区。