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Cloud implementation of Xenbase the Xenopus model organism knowledgebase

Xenbase Xenopus模型生物知识库的云实现

基本信息

批准号：
10824813
负责人：
PETER D VIZE
金额：
$ 23.83万
依托单位：
CINCINNATI CHILDRENS HOSP MED CTR
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-06-01 至 2026-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10824813
关键词：
Acceleration Administrative Supplement Animal Model Award Biological Biomedical Research Collaborations Communities Consumption Cost Savings Data Data Set Ensure Environment FAIR principles Genes Genomics Goals Growth Health Human Individual Infrastructure Knowledge Link Maintenance Mission Ontology Outcome Parents Performance Play Privatization Publications Research Research Personnel Resources Role Running Security Series Services Speed System Testing Time Translating Translations Universities Update Visualization software XenBase Xenopus bioinformatics tool biomedical resource cost data integration data management data tools design empowerment end of life experimental study flexibility genome resource human disease human model improved interoperability knowledgebase large datasets large scale data migration model organism ontology development parent grant relational database repository system architecture tool user-friendly virtual machine web-accessible

项目摘要

PROJECT SUMMARY Xenbase.org, the Xenopus model organism knowledgebase, is a web accessible resource that integrates the vast and diverse genomic and biological data from Xenopus research. The parent award to this supplement application is 2P41HD064556, 5/13/2021-04/30/2026 (PIs AM Zorn and PD Vize). Our mission is to accelerate the translation of Xenopus research into knowledge that will improve human health. We aim to empower Xenopus research and enhance the impact of Xenopus data in the broader biomedical community. Animal models such as Xenopus are essential for biomedical research and have led to a wealth of discoveries. In this post genomic era with thousands of scientific publications annually and the exponential growth of “omic” datasets, resources such as Xenbase are essential to translate this vast body of data into meaningful biological syntheses. Xenbase is the only central repository for the enormous amount of data generated from research using Xenopus. Our relational database and user-friendly interface allow investigators to quickly interrogate and link different data types in ways that would otherwise be difficult, time consuming, or impossible. Xenbase implements the FAIR data management principles that aim to make data findable, accessible, interoperable and reusable. Xenbase enhances the value of Xenopus data through high quality curation, ontology development, data integration, bioinformatics tools optimized for Xenopus experiments, and by linking Xenopus data to humans and other model organisms. Xenbase plays an indispensable role in making Xenopus data accessible to the broader biomedical community by continually providing annotated data updates to many organizations such as NCBI, UniProt, Ensembl the Alliance of Genome Resources (AGR) and other model organism knowledgebases (MOKs). Xenbase has over 1,800 registered users with ~1 million pageviews a year and ~50 unique visitors per weekday. The goals of the parent grant are to: Aim1 Maintain Xenbase, Curate and Disseminate Xenopus research data Aim 2 Enhance support for Xenopus models of human diseases Aim 3 Enhance Integrated Omics support The goal of this administrative supplement is to migrate Xenbase from a suite of physical virtual machines to a public AWS cloud. We will then perform a series of reiterative tests and improvements to enhance system reliability, performance, security and enhance large-scale data tools.

项目摘要 Xenbase.org，非洲爪蟾模式生物知识库，是一个网络可访问的资源，从非洲爪蟾研究中获得的大量多样的基因组和生物学数据。父母对这种补助的奖励申请为2P41HD 064556，2021年5月13日至2026年4月30日（PI AM Zorn和PD Vize）。我们的使命是将非洲爪蟾的研究成果转化为能够改善人类健康的知识。我们的目标是非洲爪蟾研究和增强非洲爪蟾数据在更广泛的生物医学界的影响。动物像非洲爪蟾这样的模型对于生物医学研究来说是必不可少的，并导致了大量的发现。在这后基因组时代，每年有数千篇科学出版物，“omic”的指数增长数据集，资源，如Xenbase是必不可少的，以转化为有意义的生物合成。Xenbase是唯一一个存储大量研究数据的中央存储库使用Xenopus。我们的关系数据库和用户友好的界面使调查人员能够快速询问并以其他方式将不同的数据类型链接起来，否则将是困难的、耗时的或不可能的。Xenbase 实施FAIR数据管理原则，旨在使数据可查找、可访问、可互操作并且可重复使用。Xenbase通过高质量的策展、本体论增强了Xenopus数据的价值开发，数据集成，为非洲爪蟾实验优化的生物信息学工具，并通过链接人类和其他模式生物的数据。Xenbase在使通过不断提供注释数据，使更广泛的生物医学界可以访问Xenopus数据更新到许多组织，如NCBI，UniProt，Ensembl基因组资源联盟（AGR）以及其他模式生物知识库（MOK）。Xenbase拥有超过1，800名注册用户，一年的浏览量和每个工作日约50个独立访问者。父母补助金的目标是：目标1维护Xenbase，整理和传播非洲爪蟾研究数据目的2加强对人类疾病爪蟾模型的支持目标3加强综合组学支持此管理补充的目标是将Xenbase从一套物理虚拟机迁移到公共AWS云。然后，我们将进行一系列的重复测试和改进，以增强系统可靠性、性能、安全性和增强大规模数据工具。