Knowledgebase of Escherichia coli Genome and Metabolism

大肠杆菌基因组和代谢知识库

基本信息

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
项目类别：
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

项目摘要

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.

项目概要 SRI International 和一组合作者提议进一步开发大肠杆菌 EcoCyc 数据库 (DB)。 EcoCyc 现在并将继续免费、公开地提供，并且科学家可以通过互联网访问，因为可下载的数据文件，以及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了 EcoCyc；它已被引用 4,939 次，从 2019 年起—— 2021 年，平均每年有 94,800 名用户访问 EcoCyc 网站，作为一般参考来源。大肠杆菌对于实验生物学家来说尤其适用于功能基因组实验的分析。该数据库为正在进行大肠杆菌代谢工程师全球研究的计算生物学家提供服务；开发化学品生产的新方法，包括生物燃料；以及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连接也使用 DB。我们将持续更新 EcoCyc，以反映有关基因、代谢途径、这些重要模式生物的调控相互作用将被整合到生物医学中。学术文献和大规模实验，例如基因必要性、支持生长的营养物质的数据，我们将继续全面、持续地努力完善稳态代谢。通过针对许多生长和非生长条件验证模型预测来建立这些生物体的网络模型野生型和敲除菌株的生长将在抗微生物药物中得到应用。发现和代谢工程，模型开发过程将带来许多改进生态数据库。我们将开展一项新的工作来整理除由我们服务的菌株之外的大肠杆菌菌株的基因和蛋白质 EcoCyc 已对数千个大肠杆菌菌株进行了测序；但在许多情况下，它们的基因组注释很低。我们将把来自 EcoCyc 和其他大肠杆菌菌株的精选基因注释投射到这些菌株的直向同源物中。 BioCyc DB 中数百种其他大肠杆菌菌株的基因，从而显着提高了注释质量以具有成本效益的方式处理其他大肠杆菌菌株。该项目还将扩展用于查询和分析EcoCyc的Pathway Tools软件，例如添加一个用于将新策划的基因和蛋白质注释投影到其他大肠杆菌菌株中的直向同源物的工具。