The MetaCyc & BioCyc Pathway/Genome Databases

元循环

• 批准号: 10021432
• 负责人: Ron Caspi
• 金额: $ 100.57万
• 依托单位: SRI INTERNATIONAL
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-06-19 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10021432
• 关键词: Address; Algorithms; Animal Model; Area; Bacteria; Bacterial Genes; Bacterial Genome; Basic Science; Biochemical; Biochemical Pathway; Bioinformatics; Chemicals; Collection; Communities; Computer software; Consult; Data; Data Analyses; Data Files; Data Set; Databases; Disease; Doctor of Philosophy; Encyclopedias; Enzymes; Filler; Foundations; Funding; Gene Cluster; Genes; Genetic; Genome; Goals; Gold; Horizontal Gene Transfer; Human; Human Microbiome; International; Joints; Letters; Life; Literature; Maps; Metabolic; Metabolic Pathway; Metabolism; Methods; Microbiology; Modeling; Modernization; Operon; Organism; Pathway interactions; Pharmaceutical Preparations; Phenotype; Prokaryotic Cells; Publications; Reaction; Reporting; Request for Applications; Research; Research Personnel; Resources; Route; Software Tools; Source; Speed; Students; Systems Biology; Time; Visualization; bacterial metabolism; base; comparative; complement pathway; computational pipelines; drug development; drug discovery; gene function; genome database; genome-wide; improved; interest; metabolic engineering; microbial genome; next generation; operation; outreach; pathway tools; prediction algorithm; tool; user-friendly; web portal; web services; web site

7 Project Summary The project objective is to develop a bioinformatics foundation for deciphering and modeling the metabolic networks of organisms with fully sequenced genomes, in support of drug discovery, metabolic engineering, systems biology, and basic science. Our approach is based on a gold-standard metabolic DB, MetaCyc, which is curated by Ph.D.-level biologists, from the experimental literature. A second objective is to further develop BioCyc, an evolving collection of Pathway/Genome Databases for 14,560 sequenced prokaryotic genomes. BioCyc is a premier prokaryotic genome web portal because of its comprehensive coverage of prokaryotic genomes; its integration of multiple information sources; its extensive and user-friendly bioinformatics search, visualization, and analysis tools; and its distribution of data via multiple access channels. We have four specific aims. (1) To expand MetaCyc, a highly curated multi-organism database of metabolic pathways and enzymes that serves as an encyclopedic reference of metabolic information. MetaCyc can be used to predict the metabolic pathway complement of an organism from its sequenced genome, and is a foundation for metabolic modeling. Information about experimentally determined metabolic pathways and enzymes will be curated into MetaCyc from the biomedical literature, with a focus on prokaryotic pathways. (2) To computationally generate extended versions of BioCyc, a collection of organism-specific Pathway/Genome Databases for completely sequenced prokaryotes and model organisms that includes predicted metabolic pathways, predicted metabolic pathway hole fillers, and predicted operons. We will curate the human metabolic database within BioCyc, as well as databases for important organisms in the human microbiome. (3) To enhance the PTools software that supports the querying, visualization, and analysis of MetaCyc and BioCyc data to include a more accurate metabolic pathway prediction algorithm, a new visualization of genome-scale metabolic networks, and a new set of comparative operations. We will also enhance the scalability of the software, and modernize its graphics. (4) To make MetaCyc and BioCyc available to the scientific community through a web portal and via downloadable data files and software.

7项目总结 该项目的目标是建立一个生物信息学基础，用于破译和建模具有完全测序基因组的生物体的代谢网络，以支持药物发现，代谢工程，系统 生物学和基础科学。我们的方法基于黄金标准的代谢数据库MetaCyc，由 博士学位-水平的生物学家，从实验文献。第二个目标是进一步开发BioCyc，一种不断发展的 收集了14，560个测序的原核基因组的途径/基因组数据库。BioCyc是一个主要的原核基因组门户网站，因为它全面覆盖了原核基因组;它整合了多种 信息来源;其广泛和用户友好的生物信息学搜索，可视化和分析工具;以及其 通过多个接入信道分发数据。 我们有四个具体目标。(1)为了扩展MetaCyc，一个高度策划的多生物体代谢数据库， 作为代谢信息的植物学参考的途径和酶。MetaCyc可用于 从测序的基因组中预测生物体的代谢途径， 用于代谢建模。关于实验确定的代谢途径和酶的信息将 从生物医学文献中整理成MetaCyc，重点是原核途径。(2)为了通过计算生成BioCyc的扩展版本，BioCyc是生物体特异性途径/基因组数据库的集合， 完全测序的原核生物和模式生物，包括预测的代谢途径，预测 代谢途径空穴填充物和预测的操纵子。我们将在BioCyc中管理人类代谢数据库，以及人类微生物组中重要生物的数据库。(3)增强PTools软件 支持MetaCyc和BioCyc数据的查询、可视化和分析， 代谢途径预测算法，一种新的可视化基因组规模的代谢网络，和一个新的集 比较业务。我们还将增强软件的可扩展性，并使其图形现代化。(4)到 通过门户网站和可下载数据向科学界提供MetaCyc和BioCyc 文件和软件。