Development of the www.EcoliCommunity.org Information Resource

www.EcoliCommunity.org 信息资源的开发

• 批准号: 7116641
• 负责人: BARRY L WANNER
• 金额: $ 107.76万
• 依托单位: PURDUE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-06-01 至 2009-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7116641
• 关键词: Escherichia coli; Escherichia coli k12; Internet; bioinformatics; cooperative study; information dissemination; information retrieval; information system analysis; information systems; microorganism resource /registry

DESCRIPTION (provided by applicant): Basic knowledge of the biochemistry, molecular biology, and genetics of Escherichia coli K-12 may be more advanced than for any other organism. This information ranges from environmental physiologic responses down to the atomic level and its the sheer volume makes it exceedingly difficult, even for experts, to fully grasp and utilize. While many databases, websites, and computational tools enable access to and interrogation of these biological data, none is comprehensive and many gaps exist. The quality and quantity of these resources vary; many have redundant, conflicting, and out-of-date information. Since data typically cannot be traced back to sources, reliability is constantly in question. Existing information systems are disorganized, overwhelmed by current knowledge, and not prepared for handling new information from high-throughput experimentation (genome-wide transcription, translation, and metabolite profiling, large-scale structural biology, enhanced imaging of living cells, and the like). The proposed integrated "one-stop-shopping" E. coli community information Resource, EcoliHub, will permit full use of existing knowledge and enable new discoveries for a deeper understanding of life processes. These tools and the advances they allow will greatly impact human health both through application to pathogenic bacteria, especially enteropathogenic E. coli, Shigella, and Salmonella species, and because many cellular processes are universal. This EcoliHub Resource builds on our prototype database designed for seamless and transparent bi-directional connections with cooperating interoperable resources (EcoCyc, Genobase and the OU microarray DB), and with major biological databases (e.g., ERIC, NCBI Entrez Gene, UniProt, and KEGG). EcoliHub will provide a chat room to facilitate community-driven developments that meet the needs of the users. It will offer on-the-fly computational tools for molecular and structural analysis; like 3D-PSSM, BLAST/PSI-BLAST, BLOCKS, Pfam, and PredictProtein. The Resource will maintain a depository of related E. coli informatics from specialized databases including Brenda, GeneMark, GenProtEC, GO, LipoP, MEROPS, PORES, RegulonDB, Superfamily, and TransportDB. Schemata will be designed to annotate and track changes within the information sources. A module for biosamples (strains, plasmids, etc.) will facilitate materials acquisition from national repositories (the Coli Genetic Stock Center and others). Interoperation and provision of information will be achieved with web services and a web-based architecture will provide public access to the Resource, including intuitive software for data mining and high-throughput functional studies.

描述（由申请人提供）：大肠杆菌K-12的生物化学，分子生物学和遗传学的基本知识可能比任何其他生物更先进。这些信息的范围从环境生理反应到原子水平，其庞大的数量使得即使是专家也很难完全掌握和利用。虽然许多数据库、网站和计算工具能够访问和查询这些生物数据，但没有一个是全面的，存在许多差距。这些资源的质量和数量各不相同；很多都有冗余、冲突和过时的信息。由于数据通常无法追溯到来源，因此可靠性一直存在问题。现有的信息系统杂乱无章，被现有的知识淹没，并且没有准备好处理来自高通量实验（全基因组转录、翻译和代谢物分析、大规模结构生物学、活细胞增强成像等）的新信息。拟议的综合“一站式”大肠杆菌社区信息资源EcoliHub将允许充分利用现有知识，并为更深入地了解生命过程提供新的发现。这些工具及其带来的进步将极大地影响人类健康，因为它们可以应用于致病菌，特别是肠致病性大肠杆菌、志贺氏菌和沙门氏菌，而且许多细胞过程是普遍存在的。这个EcoliHub资源建立在我们的原型数据库的基础上，设计用于与合作互操作资源（EcoCyc， Genobase和OU微阵列数据库）以及主要生物数据库（例如ERIC， NCBI Entrez Gene， UniProt和KEGG）进行无缝透明的双向连接。EcoliHub将提供一个聊天室，以促进社区驱动的开发，满足用户的需求。它将为分子和结构分析提供实时计算工具；如3D-PSSM， BLAST/PSI-BLAST， BLOCKS， Pfam和PredictProtein。该资源将维护来自Brenda、GeneMark、GenProtEC、GO、LipoP、MEROPS、pore、RegulonDB、Superfamily和TransportDB等专业数据库的相关大肠杆菌信息库。模式将被设计为注释和跟踪信息源中的更改。生物样品（菌株，质粒等）模块将方便从国家储存库（大肠杆菌遗传库存中心等）获取材料。互操作和信息提供将通过网络服务实现，基于网络的体系结构将为公众提供对资源的访问，包括用于数据挖掘和高通量功能研究的直观软件。