Knowledgebase of Escherichia coli Genome and Metabolism

大肠杆菌基因组和代谢知识库

• 批准号: 10716050
• 负责人: PETER D KARP
• 金额: $ 145.53万
• 依托单位: SRI INTERNATIONAL
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-30 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10716050
• 关键词: Acceleration; Acetylation; Australia; Bacteria; Biochemical Pathway; Bioinformatics; Biomedical Research; Chemicals; Climate; Collection; Communities; Companions; Complex; Computational Biology; Computer software; Computers; Computing Methodologies; Consult; Data; Data Collection; Data Files; Data Set; Databases; Discipline; Documentation; Education; Ensure; Epigenetic Process; Escherichia coli; Escherichia coli O157:H7; Escherichia coli Proteins; Funding; Future; Genes; Genetic; Genome; Gram-Negative Bacteria; Growth; Human Microbiome; Information Resources; International; Internet; Knock-out; Knowledge; Letters; Literature; Metabolic; Metabolic Pathway; Metabolism; Methods; Mexico; Microbiology; Mission; Modeling; Molecular Machines; Nutrient; Operon; Organism; Orthologous Gene; Planet Earth; Process; Production; Proteins; Publications; Publishing; Reaction; Regulation; Request for Applications; Research; Research Personnel; Resources; Science; Scientist; Shiga Toxin; Site; Software Tools; Source; System; Time; Training; Triage; United States National Institutes of Health; Universities; Update; Validation; Visit; Visualization; Work; Writing; antimicrobial drug; computerized tools; cost effective; drug discovery; experimental study; falls; functional genomics; gene product; genome annotation; improved; innovation; knowledge integration; knowledgebase; metabolic engineering; model development; model organism; model organisms databases; operation; outreach; pathogenic bacteria; pathway tools; phenotypic data; predictive modeling; promoter; quality assurance; software development; tool; web site

Project Summary SRI International and a group of collaborators propose to further develop the Escherichia coli EcoCyc database (DB). EcoCyc is and will continue to be freely and openly available, and is accessible to scientists through the Internet, as downloadable data files, and as a downloadable software application. Scientists from multiple disciplines make wide use of EcoCyc; it has been cited 4,939 times, and from 2019– 2021, an average of 94,800 users per year visited the EcoCyc website. It serves as a general reference source on E. coli for experimental biologists and is particularly useful for the analysis of functional-genomics experiments. The DB serves computational biologists who are undertaking global studies of E. coli; metabolic engineers who are developing new methods for chemicals production, including biofuels; and researchers and bioinformaticists who are using EcoCyc as the gold-standard dataset to develop new computational methods, including the prediction of operons, promoters, and protein functional linkages. Educators also use the DB. We will update EcoCyc in an ongoing fashion to reflect new information about the genes, metabolic pathways, and regulatory interactions of these important model organisms. Information will be integrated from the biomed- ical literature and from large-scale experiments, such as data on gene essentiality, on nutrients supporting growth, and on protein interactions. We will continue a comprehensive and ongoing effort to refine steady-state metabolic network models of these organisms by validating model predictions against many conditions of growth and non- growth for wildtype and knock-out strains. The resulting models will have applications in anti-microbial drug discovery and metabolic engineering, and the model development process will lead to many improvements in the EcoCyc DB. We will launch a new effort to curate the genes and proteins of E. coli strains other than the strain served by EcoCyc. Thousands of E. coli strains have been sequenced; yet in many cases, their genome annotations are of low quality. We will project curated gene annotations from EcoCyc and from other E. coli strains to orthologs of those genes in the BioCyc DBs for hundreds of other E. coli strains, thus significantly improving the annotation quality of other E. coli strains in a cost-effective fashion. The project will also expand the Pathway Tools software used to query and analyze EcoCyc, such as adding a tool for projecting newly curated gene and protein annotations to orthologs in other E. coli strains.

项目摘要 SRI International和一组合作者建议进一步开发大肠杆菌EcoCyc数据库（DB）。 EcoCyc现在和将来都是免费和公开的，科学家可以通过互联网访问， 可下载的数据文件，并作为可下载的软件应用程序。 来自多个学科的科学家广泛使用EcoCyc;它已被引用4，939次，从2019年开始- 于二零二一年，EcoCyc网站平均每年有94，800名用户浏览。它作为一个通用的参考源， E.大肠杆菌的实验生物学家，特别是用于功能基因组学实验的分析。 DB为正在进行全球E研究的计算生物学家提供服务。大肠杆菌;代谢工程师 开发新的化学品生产方法，包括生物燃料;研究人员和生物信息学家， 正在使用EcoCyc作为黄金标准数据集来开发新的计算方法，包括预测 操纵子、启动子和蛋白质功能键。教育工作者也使用DB。 我们将持续更新EcoCyc，以反映有关基因，代谢途径， 以及这些重要模式生物之间的相互调节作用。信息将从生物医学- 科学文献和大规模实验的数据，如基因重要性数据，支持生长的营养素数据， 和蛋白质相互作用。我们将继续全面和持续的努力，以完善稳态代谢 这些生物的网络模型，通过验证模型预测对许多条件的增长和非 野生型和敲除菌株的生长。所得到的模型将在抗微生物药物中得到应用 发现和代谢工程，模型开发过程将导致许多改进， EcoCyc DB. 我们将发起一项新的努力，以策展的基因和蛋白质的E。大肠杆菌菌株以外的菌株 EcoCyc。成千上万的E。大肠杆菌菌株已经测序;但在许多情况下，它们的基因组注释是低的， 质量.我们将从EcoCyc和其他E.大肠杆菌菌株的直系同源物 BioCyc数据库中的数百个其他E.大肠杆菌菌株，从而显着提高注释质量 其它大肠大肠杆菌菌株以具有成本效益的方式。 该项目还将扩展用于查询和分析EcoCyc的Pathway Tools软件，例如添加 用于将新策划的基因和蛋白质注释投射到其他大肠杆菌中的直系同源物的工具。大肠杆菌菌株。