The MetaCyc and BioCyc Pathway/Genome Databases
MetaCyc 和 BioCyc 通路/基因组数据库
基本信息
- 批准号:7260111
- 负责人:
- 金额:$ 90.38万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2007
- 资助国家:美国
- 起止时间:2007-06-19 至 2011-04-30
- 项目状态:已结题
- 来源:
- 关键词:AlgorithmsBacteriaBiochemicalBiochemical PathwayBioinformaticsChemical StructureCodeCollectionCommunitiesComplementComputer softwareComputersDataDatabasesDepthDevelopmentDiseaseDisruptionDoctor of PhilosophyEducation and OutreachEngineeringEnzymesFillerFoundationsFruitGenesGenomeGenomicsGoldHarvestImageryInternationalInternetKnowledgeLiteratureMetabolicMetabolic PathwayMetabolismMicrobeModelingNatural regenerationNumbersOnline SystemsOntologyOperonOrganismPathway interactionsPharmaceutical PreparationsPlantsProceduresReactionResearchScienceServicesSiteSoftware ToolsSourceSpeedStandards of Weights and MeasuresStudentsSystems BiologyUniversitiesbasecomparativecomplement pathwaycomputerized data processingdesigndrug developmentdrug discoveryenzyme pathwaygenome databasegenome sequencingimprovedinnovationkillingsmicrobialmicrobial genomenext generationtoolusabilityuser-friendly
项目摘要
DESCRIPTION (provided by applicant): The long-term 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, and systems biology. Our approach is based on a gold-standard metabolic database, MetaCyc, which is curated by Ph.D.-level biologists, strictly from the experimental literature. The knowledge in MetaCyc is extended computationally to other organisms by the automated creation of hundreds of organism-specific pathway/genome databases. Our specific aims are (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 microbial and plant pathways and enzymes. (2) To computationally generate BioCyc, a collection of organism-specific pathway/genome databases for all completely sequenced microbes 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 a new pathway prediction algorithm, an improved Web site, and scalability to manage 1000 genomes. (4) To make MetaCyc and BioCyc available in several formats. The BioCyc databases will be generated through a computational pipeline using advanced and carefully validated algorithms. MetaCyc and BioCyc data will be captured within a rich database schema using pathway editing software, and made publicly available through multiple access mechanisms, including a user-friendly Web site and the BioPAX standard pathway format. Metabolic pathways form the biochemical foundation of living systems. By quickly characterizing the metabolic pathways of hundreds of microbes, this project will facilitate alterations to those pathways by metabolic engineers, such as to allow bacteria to synthesize drugs. It will speed the development of drugs that kill disease-causing bacteria by enabling identification of essential metabolic pathways for disruption.
描述(由申请人提供):长期目标是建立一个生物信息学基础,用于破译具有完全测序基因组的每个生物体的代谢网络,以支持药物发现、代谢工程和系统生物学。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精心策划,严格来自实验文献。通过自动创建数百个生物体特定途径/基因组数据库,MetaCyc 中的知识可以通过计算扩展到其他生物体。我们的具体目标是 (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,重点是微生物和植物途径和酶。 (2) 通过计算生成 BioCyc,这是所有完全测序的微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,包括新的路径预测算法、改进的网站以及管理 1000 个基因组的可扩展性。 (4) 使 MetaCyc 和 BioCyc 以多种格式提供。 BioCyc 数据库将使用先进且经过仔细验证的算法通过计算管道生成。 MetaCyc 和 BioCyc 数据将使用通路编辑软件在丰富的数据库模式中捕获,并通过多种访问机制公开提供,包括用户友好的网站和 BioPAX 标准通路格式。代谢途径构成了生命系统的生化基础。通过快速表征数百种微生物的代谢途径,该项目将促进代谢工程师对这些途径的改变,例如允许细菌合成药物。它将通过识别破坏的基本代谢途径来加速杀死致病细菌的药物的开发。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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PETER D KARP其他文献
PETER D KARP的其他文献
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{{ truncateString('PETER D KARP', 18)}}的其他基金
Knowledgebase of Escherichia coli Genome and Metabolism
大肠杆菌基因组和代谢知识库
- 批准号:
10716050 - 财政年份:2023
- 资助金额:
$ 90.38万 - 项目类别:
Development and Support of the Pathway Tools Software
Pathway Tools 软件的开发和支持
- 批准号:
10609063 - 财政年份:2021
- 资助金额:
$ 90.38万 - 项目类别:
Development and Support of the Pathway Tools Software
Pathway Tools 软件的开发和支持
- 批准号:
10404662 - 财政年份:2021
- 资助金额:
$ 90.38万 - 项目类别:
Development and Support of the Pathway Tools Software
Pathway Tools 软件的开发和支持
- 批准号:
10220624 - 财政年份:2021
- 资助金额:
$ 90.38万 - 项目类别:
Development and Support of the Pathway Tools Software
Pathway Tools 软件的开发和支持
- 批准号:
7902995 - 财政年份:2009
- 资助金额:
$ 90.38万 - 项目类别:
The MetaCyc and BioCyc Pathway/Genome Databases
MetaCyc 和 BioCyc 通路/基因组数据库
- 批准号:
7450885 - 财政年份:2007
- 资助金额:
$ 90.38万 - 项目类别:
Pathway Prediction and Assessment Integrating Multiple Evidence Types
整合多种证据类型的路径预测和评估
- 批准号:
7685518 - 财政年份:2007
- 资助金额:
$ 90.38万 - 项目类别:
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 - 财政年份:2007
- 资助金额:
$ 90.38万 - 项目类别:
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:
8471118 - 财政年份:2007
- 资助金额:
$ 90.38万 - 项目类别:
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