The MetaCyc and BioCyc Pathway/Genome Databases [SRI Proposal ECU 10-626]

MetaCyc 和 BioCyc 通路/基因组数据库 [SRI 提案 ECU 10-626]

• 批准号: 8298991
• 负责人: PETER D KARP
• 金额: $ 122.83万
• 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 2015-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8298991
• 关键词: Algorithms; Animal Model; Area; Bacteria; Bacterial Genome; Basic Science; Biochemical; Biochemical Pathway; Biochemical Reaction; Bioinformatics; Chemical Structure; Chemicals; Collection; Communities; Complement; Computer software; Consult; Data; Data Analyses; Data Files; Databases; Disease; Doctor of Philosophy; Engineering; Enzymes; Filler; Foundations; Genome; Goals; Gold; Harvest; Homo sapiens; Human Microbiome; Imagery; Institutes; International; Internet; Life; Literature; Metabolic; Metabolic Pathway; Metabolism; Methods; Microbiology; Neighborhoods; Operon; Organism; Pathway interactions; Pharmaceutical Preparations; Phenotype; Plants; Prokaryotic Cells; Proteins; Reaction; Reporting; Request for Applications; Research; Research Personnel; Scientist; Source; Speed; Students; Systems Biology; Time; Transcriptional Regulation; base; comparative; comparative genomics; drug development; drug discovery; enzyme pathway; genome database; genome sequencing; killings; novel; operation; outreach; pathway tools; tool; user-friendly; web services; web site

DESCRIPTION (provided by applicant): The project objective is to develop a bioinformatics foundation for deciphering the metabolic network of every organism with a fully sequenced genome, in support of drug discovery, metabolic engineering, systems biology, and basic science. Our approach is based on a gold-standard metabolic database, 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 5,000-10,000 sequenced prokaryotic genomes. BioCyc will become the premier source of prokaryotic genome data because of its planned comprehensive coverage of prokaryotic genomes; its integration of multiple information sources; its powerful 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. Information about experimentally determined metabolic pathways and enzymes will be curated into MetaCyc from the biomedical literature, with a focus on prokaryotic, fungal, and plant information. (2) To computationally generate 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. (3) To enhance the Pathway Tools software that supports the querying, visualization, and analysis of MetaCyc and BioCyc to include new comparative genomics capabilities; to include genome-context-based predic- tions of functionally related proteins and of novel pathways; to include a tool for iteratively browsing the reaction neighborhood of a metabolite; and to provide textual searches against multiple BioCyc databases. (4) To make MetaCyc and BioCyc available to the scientific community through a Web portal and via downloadable data files and software.

描述（由申请人提供）：该项目的目标是开发一个生物信息学基础，用于破译具有完全测序的基因组的每个生物体的代谢网络，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代谢数据库 MetaCyc，该数据库由博士级生物学家根据实验文献整理。第二个目标是进一步开发 BioCyc，这是一个不断发展的路径/基因组数据库集合，包含 5,000-10,000 个已测序的原核生物基因组。 BioCyc 由于计划全面覆盖原核生物基因组，将成为原核生物基因组数据的首要来源；多种信息源的整合；其强大且用户友好的生物信息学搜索、可视化和分析工具；及其通过多个访问通道分发数据。 我们有四个具体目标。 (1) 扩展 MetaCyc，这是一个精心策划的代谢途径和酶的多生物体数据库，可作为代谢信息的百科全书参考。 MetaCyc 可用于从生物体的基因组测序中预测其代谢途径的补充。有关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到 MetaCyc 中，重点是原核、真菌和植物信息。 (2) 通过计算生成 BioCyc，这是一个针对完全测序的原核生物和模型生物的生物体特异性途径/基因组数据库的集合，其中包括预测的代谢途径、预测的代谢途径空洞填充物和预测的操纵子。 (3) 增强支持MetaCyc和BioCyc查询、可视化和分析的Pathway Tools软件，以包含新的比较基因组学功能；包括基于基因组背景的功能相关蛋白质和新途径的预测；包括一个用于迭代浏览代谢物反应邻域的工具；并提供针对多个 BioCyc 数据库的文本搜索。 (4) 通过门户网站以及可下载的数据文件和软件向科学界提供 MetaCyc 和 BioCyc。