Development of the www.EcoliCommunity.org Information Resource

www.EcoliCommunity.org 信息资源的开发

• 批准号: 7886194
• 负责人: BARRY L WANNER
• 金额: $ 30.5万
• 依托单位: PURDUE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-31 至 2010-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7886194
• 关键词: Architecture; Award; Back; Bacteriophages; Biochemistry; Biological; Biological databases; Blast Cell; Cell division; Cell model; Cell physiology; Cells; Collaborations; Communities; Computer Assisted; Computer software; Conflict (Psychology); Data; Databases; Development; Educational workshop; Escherichia coli; Escherichia coli EHEC; Eye; Feedback; Gene Expression; Genes; Genetic; Genetic Transcription; Goals; Health; Housing; Human; Image; Imagery; Informatics; Information Resources; Information Systems; Internet; Java; Knowledge; Life; Maintenance; Microbe; Mining; Molecular; Molecular Biology; Oklahoma; Online Systems; Ontology; Organism; Pathway interactions; Phase; Physiological; Plasmids; Process; Proteins; RNA Processing; Regulation; Relative (related person); Resources; Salmonella; Scientist; Services; Shigella; Site; Source; System; Testing; Translations; Universities; Vocabulary; Work; base; computerized tools; data mining; database design; design; enteropathogenic Escherichia coli; experience; gene function; genetic element; genome-wide; grasp; improved; interoperability; meetings; member; mutant; news; pathogenic bacteria; peer; protein folding; protein protein interaction; prototype; repository; response; small molecule; structural biology; tool; user-friendly; web-accessible

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 The quality and quantity of these resources vary; many have redundant, conflicting, and out-of-date information.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)：对大肠杆菌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体都要先进。这些信息的范围从环境生理反应到原子水平，其庞大的数量使其极其困难，即使对专家来说，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询问这些生物数据，但没有一个是全面的，存在许多空白。这些资源的质量和数量各不相同；许多资源包含冗余、冲突和过时的信息。由于数据通常无法追溯到来源，可靠性一直受到质疑。现有的信息系统杂乱无章，被现有的知识淹没，没有准备好处理来自高通量实验的新信息(全基因组转录、翻译和代谢物图谱、大规模结构生物学、活细胞的增强成像等)。拟议的一站式综合大肠杆菌社区信息资源，EcoliHub，将允许充分利用现有知识，并使新的发现，以更深入地了解生命过程。这些工具及其允许的进步将通过应用于致病细菌，特别是肠源性大肠杆菌、志贺氏菌和沙门氏菌，以及因为许多细胞过程是普遍的，从而极大地影响人类健康。该EcoliHub资源建立在我们的原型数据库的基础上，专为与合作的可互操作资源(EcoCyc、Genobase和OU微阵列数据库)以及主要的生物数据库(例如Eric、NCBI Entrez gene、UniProt和KEGG)进行无缝和透明的双向连接而设计。EcoliHub将提供聊天室，以促进满足用户需求的社区驱动的开发。它将为分子和结构分析提供即时计算工具，如3D-PSSM、BLAST/PSI-BLAST、BLOCKS、Pfam和PredicatedProtein。该资源将维护来自专业数据库的相关大肠杆菌信息库，包括Brenda、GeneMark、GenProtEC、GO、LiPOP、Merops、毛孔、RegulonDB、SuperFamily和TransportDB。模式将被设计为注释和跟踪信息源内的变化。用于生物样本(菌株、质粒等)的模块将促进从国家储存库(科利基因储存中心和其他机构)获取材料。将通过网络服务实现互操作和提供信息，一个基于网络的架构将为公众提供对资源的访问，包括用于数据挖掘和高吞吐量功能研究的直观软件。

项目成果

EcoliWiki: a wiki-based community resource for Escherichia coli.

• DOI: 10.1093/nar/gkr880
• 发表时间: 2012-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: McIntosh BK;Renfro DP;Knapp GS;Lairikyengbam CR;Liles NM;Niu L;Supak AM;Venkatraman A;Zweifel AE;Siegele DA;Hu JC
• 通讯作者: Hu JC

Comparative genomics of small RNAs in bacterial genomes.

• DOI: 10.1089/omi.2006.0005
• 发表时间: 2007
• 期刊: Omics : a journal of integrative biology
• 作者: S. Luban;D. Kihara

The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology.

• DOI: 10.1186/1471-2164-11-470
• 发表时间: 2010-08-11
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Rajagopala SV;Yamamoto N;Zweifel AE;Nakamichi T;Huang HK;Mendez-Rios JD;Franca-Koh J;Boorgula MP;Fujita K;Suzuki K;Hu JC;Wanner BL;Mori H;Uetz P
• 通讯作者: Uetz P

Protein-protein docking using region-based 3D Zernike descriptors.

• DOI: 10.1186/1471-2105-10-407
• 发表时间: 2009-12-09
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Venkatraman V;Yang YD;Sael L;Kihara D
• 通讯作者: Kihara D

Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP.

• DOI: 10.1186/1471-2105-11-265
• 发表时间: 2010-05-19
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Hawkins T;Chitale M;Kihara D
• 通讯作者: Kihara D