Enhanced Echinobase: A Community Genomics Research Resource For The Future

增强型 Echinobase：未来的社区基因组学研究资源

• 批准号: 10715578
• 负责人: CHARLES A. ETTENSOHN
• 金额: $ 78.69万
• 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/10715578
• 关键词: ATAC-seq; Access to Information; Address; Atlases; Biological Models; Cells; Code; Communication; Communities; Computer software; Consultations; Consumption; Controlled Vocabulary; DNA methylation profiling; Data; Databases; Development; Developmental Gene; Disease; EchinoBase; Echinodermata; Embryonic Development; Experimental Models; FAIR principles; Fostering; Funding; Future; Gene Expression; Genes; Genetic Transcription; Genome; Genomics; Goals; Health; Human; Infrastructure; Investments; Knowledge; Letters; Link; Logic; Mission; Names; Nomenclature; Ontology; Organism; Pattern; Performance; Play; Process; Research; Research Personnel; Resources; Role; Sea Urchins; Systems Analysis; Taxonomy; Time; Tissues; United States National Institutes of Health; Untranslated RNA; Update; Visualization software; Work; XCL1 gene; XenBase; base; bioinformatics tool; cost; data integration; data management; data mining; data sharing; design; empowerment; gene regulatory network; genome resource; genomic data; improved; interoperability; knowledge base; knowledgebase; model organism; ontology development; predictive modeling; relational database; repository; tool; transcriptome sequencing; usability; user-friendly; web app; web site; web-accessible

SUMMARY OF OVERALL COMPONENT Enhanced Echinobase: A Community Genomics Research Resource for the Future Echinobase (Echinobase.org) is the central repository and web-accessible resource for all of the diverse genomic data types produced by biologists working with echinoderms. Echinobase was cloned from Xenbase to enhance database functionality, web application capabilities, and performance, all at a fraction of the cost of doing this independently. A key added feature developed through this work are database modules that support curation and searches of gene expression data. The look and feel of Echinobase is unique, and is tailored to its user base including the creation of a multi-species viewer. The website provides rapid integrated capabilities for search, view and download of 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. The strengths of this experimental model will continue to make it a preeminent system for the analysis of the genomic control of embryogenesis and for analyses of developmental gene regulatory networks (GRNs) to reveal the mechanistic links between the genome and development and consequently the genomic basis of congenital diseases.

整体组成部分摘要 增强型 Echinobase：未来的社区基因组学研究资源 Echinobase (Echinobase.org) 是所有不同领域的中央存储库和可通过网络访问的资源 由研究棘皮动物的生物学家产生的基因组数据类型。 Echinobase 是从 Xenbase 克隆的 增强数据库功能、Web 应用程序功能和性能，而成本只是 独立地做这件事。通过这项工作开发的一个关键附加功能是支持 基因表达数据的管理和搜索。 Echinobase 的外观和感觉是独一无二的，并且是根据其需求量身定制的 用户群，包括创建多物种查看器。网站提供快速集成能力 用于搜索、查看和下载一系列数据类型以支持自己的研究。棘皮动物就是其中之一 后口动物中只有三个主要门，因此该分支中的物种包括 身体计划的巨大分类多样性。棘皮动物物种是强大的模型系统 了解基因组控制发育的过程。本实验的优点 该模型将继续使其成为分析胚胎发生的基因组控制的卓越系统 以及对发育基因调控网络（GRN）的分析，以揭示基因之间的机制联系 基因组和发育，以及先天性疾病的基因组基础。

项目成果

Integration of 1:1 orthology maps and updated datasets into Echinobase.

将 1:1 直系图和更新的数据集集成到 Echinobase 中。

• 发表时间: 2021-05-19
• 作者: Foley, Saoirse;Ku, Carolyn;Arshinoff, Brad;Lotay, Vaneet;Karimi, Kamran;Vize, Peter D;Hinman, Veronica
• 通讯作者: Hinman, Veronica

Genome-wide identification and spatiotemporal expression analysis of cadherin superfamily members in echinoderms.

棘皮动物钙粘蛋白超家族成员的全基因组鉴定和时空表达分析。

• 发表时间: 2023-12-20
• 影响因子: 4.1
• 作者: Chess, Macie M;Douglas, William;Saunders, Josiah;Ettensohn, Charles A
• 通讯作者: Ettensohn, Charles A

Echinobase: a resource to support the echinoderm research community.

Echinobase：支持棘皮动物研究社区的资源。

• 发表时间: 2024-01-23
• 影响因子: 3.3
• 作者: Telmer, Cheryl A;Karimi, Kamran;Chess, Macie M;Agalakov, Sergei;Arshinoff, Bradley I;Lotay, Vaneet;Wang, Dong Zhuo;Chu, Stanley;Pells, Troy J;Vize, Peter D;Hinman, Veronica F;Ettensohn, Charles A
• 通讯作者: Ettensohn, Charles A

Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms.

Echinobase：利用现有的模式生物数据库构建支持棘皮动物基因组学和生物学研究的知识库。

• 发表时间: 2022
• 影响因子: 14.9
• 作者: Arshinoff, Bradley I;Cary, Gregory A;Karimi, Kamran;Foley, Saoirse;Agalakov, Sergei;Delgado, Francisco;Lotay, Vaneet S;Ku, Carolyn J;Pells, Troy J;Beatman, Thomas R;Kim, Eugene;Cameron, R Andrew;Vize, Peter D;Telmer, Cheryl A;Croce, Jenifer
• 通讯作者: Croce, Jenifer

A nomenclature for echinoderm genes.

棘皮动物基因的命名法。

• 发表时间: 2021
• 作者: Beatman, Thomas R;Buckley, Katherine M;Cary, Gregory A;Hinman, Veronica F;Ettensohn, Charles A
• 通讯作者: Ettensohn, Charles A