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xBASE: a bioinformatics resource for the AgriFood bacteriology community

xBASE：农业食品细菌学界的生物信息学资源

基本信息

批准号：
BB/E011179/1
负责人：
Mark Pallen
金额：
$ 99.09万
依托单位：
University of Birmingham
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2007
资助国家：
英国
起止时间：
2007 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FE011179%2F1
关键词：
xBASE bioinformatics resource AgriFood bacteriology

项目摘要

Bacteria play important roles at every stage in the human food chain, from improving the productivity of the soil to infecting the human consumer. The advent of genome sequencing, functional genomics and systems biology brings the promise of unparalleled progress in the bacteriology of the human food chain. However, bacteriologists are drowning in in a sea of data. Hundreds of bacterial genome projects have been completed or are underway. On top of this, we are now threatened with a novel deluge of data from systems biology studies . Unless the average bacteriologist is able to exploit the new flood of genomics data, the whole genomics enterprise risks becoming an expensive molecular stamp-collecting exercise. In recent years, we have met this challenge by providing bacteriologists with a set of user-friendly tools for visualising, analysing and exploiting genome sequence data from bacteria of importance to the human food chain. Our most recent effort is coliBASE, a web site and database dedicated to the comparative genomics of E. coli and related bacteria of relevance in the AgriFood context. As evidence of its success, this site is receiving >1000 visitors a month. In this proposal, we aim to take these facilities into the second decade of the twenty-first century by the development of xBASE, a series of taxon-specific databases, in which we add breadth (by covering a wider range of organisms) and add depth (by adding additional analytical and visualization tools, including new tools to cope with data from bacterial Systems Biology and meta-genomics projects) to our current repertoire.

细菌在人类食物链的每个阶段都发挥着重要作用，从提高土壤的生产力到感染人类消费者。基因组测序、功能基因组学和系统生物学的出现，为人类食物链细菌学带来了前所未有的进步。然而，细菌学家淹没在数据的海洋中。数百个细菌基因组计划已经完成或正在进行中。最重要的是，我们现在受到来自系统生物学研究的大量数据的威胁。除非普通的细菌学家能够利用新的基因组学数据，否则整个基因组学事业就有可能成为昂贵的分子印章收集活动。近年来，我们通过为细菌学家提供一套用户友好的工具来可视化，分析和利用对人类食物链重要的细菌的基因组序列数据来应对这一挑战。我们最近的努力是coliBASE，一个致力于大肠杆菌比较基因组学的网站和数据库。大肠杆菌和相关的细菌在农业食品背景下的相关性。作为其成功的证据，该网站每月接待超过1000名访问者。在这项提案中，我们的目标是通过开发xBASE（一系列分类特定的数据库）将这些设施带入21世纪的第二个十年，在这些数据库中，我们增加了广度（通过覆盖更广泛的生物体）和深度（通过增加额外的分析和可视化工具，包括科普细菌系统生物学和元基因组学项目数据的新工具）。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Calculating orthologs in bacteria and Archaea: a divide and conquer approach.

DOI：
10.1371/journal.pone.0028388
发表时间：
2011
期刊：
PloS one
影响因子：
3.7
作者：
Halachev MR;Loman NJ;Pallen MJ
通讯作者：
Pallen MJ

EntrezAJAX: direct web browser access to the Entrez Programming Utilities

EntrezAJAX：直接通过 Web 浏览器访问 Entrez 编程实用程序

DOI：
10.1186/1751-0473-5-6
发表时间：
2010
期刊：
Source Code for Biology and Medicine
影响因子：
0
作者：
Loman N
通讯作者：
Loman N

Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England.

DOI：
10.1186/s13073-014-0070-x
发表时间：
2014
期刊：
Genome medicine
影响因子：
12.3
作者：
Halachev MR;Chan JZ;Constantinidou CI;Cumley N;Bradley C;Smith-Banks M;Oppenheim B;Pallen MJ
通讯作者：
Pallen MJ

Defining bacterial species in the genomic era: insights from the genus Acinetobacter.