Enhanced Echinobase: A Community Genome Resource for the Future

增强型 Echinobase：未来的社区基因组资源

• 批准号: 10442594
• 负责人: CHARLES A. ETTENSOHN
• 金额: $ 53.83万
• 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/10442594
• 关键词: ATAC-seq; Anatomy; Animal Model; Biological Models; Biology; Birth; ChIP-seq; Communities; Controlled Vocabulary; Custom; Data; Databases; Defect; Development; Developmental Gene; Developmental Process; EchinoBase; Echinodermata; Educational workshop; Elements; Embryonic Development; Ensure; Experimental Models; Future; Gene Expression; Genes; Genetic Variation; Genome; Genomics; Goals; Inherited; Internet; Knowledge; Lead; Letters; Link; Literature; Logic; Modeling; Ontology; Orthologous Gene; Paper; Performance; Process; Proteome; Publications; Research; Research Personnel; Research Support; Resources; Role; Scientist; Sea Urchins; Structure; Surveys; System; Systems Analysis; Taxonomy; Text; Time; Training; Untranslated RNA; Update; Vocabulary; Work; XenBase; base; cost; data integration; design; functional genomics; gene regulatory network; genome resource; genomic data; improved; network models; predictive modeling; repository; spatiotemporal; syntax; transcriptome; web app; web interface; web site; web-accessible

ENHANCED ECHINOBASE: A COMMUNITY GENOMICS RESEARCH RESOURCE FOR THE FUTURE Overall Summary Echinobase (Echinobase.org) is a database that houses all of the diverse genomic data types produced by biologists working with echinoderms. It is accessed through a website that allows scientists to search, view and download a range of datatypes to empower their own research. Echinoderms are one of only three major phyla within the deuterostomes, and therefore the species within this clade encompass a large taxonomic diversity of body plans. Species of echinoderms are powerful model systems for understanding the processes by which the genome controls development. For example, they have uniquely contributed to understanding how gene expression is regulated in time and space and how networks of interacting genes, or Gene Regulatory Networks (GRNs) control development. The proposal here will migrate current Echinobase data to a customized clone of Xenbase with underlying Chado schema. As a consequence, Echinobase will inheriting enhanced database functionality, web application capabilities, and performance upgrades, all at a fraction of the cost of doing this independently. A key added feature obtained through this work will be database modules that support curation and searches of gene expression data, and thus effort is proposed to curate gene expression data to exploit this important capability. The look and feel of Echinobase will however be unique, and be tailored to its user base. A further goal of this proposal is to develop an echinoderm embryological anatomy schema using controlled vocabularies, and to improve identification of orthologous genes, not only among echinoderms but also to common reference proteomes. These initiatives follow emerging best practices, and hence ensure that Echinobase data can be readily shared with other resources. The assembly and annotation of echinoderm genomes, including the identification of both genic and noncoding regulatory features, will also be improved. Significant improvements to the curation of these genic and nongenic elements are also proposed. The new resource will also support an interactive module to model GRNs. These enhancements are directed at providing data types to support research for which the echinoderms have known strengths and where they can contribute uniquely to reveal the mechanistic links between the genome and development. The goal is to integrate these components to allow a user to readily navigate through these different data types in the different species. Changes will also be made throughout, to make this resource more useable, e.g. by controlling vocabularies, improving website design, and by providing training and workshops, in order to increase the usefulness of the resource. The improvements suggested throughout this proposal have wide community support as evidenced by results of our survey and community White Paper, boh referenced in the component, and 34 attached letters of support. 1

增强型基因组数据库：面向未来的社区基因组学研究资源