Building a Network of Plant Metabolic Pathway Databases and Communities

建立植物代谢途径数据库和社区网络

• 批准号: 0640769
• 负责人: Seung Rhee
• 金额: $ 147.79万
• 依托单位: Carnegie Institution of Washington
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-03-15 至 2013-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0640769&HistoricalAwards=false
• 关键词: Building; Network; Plant; Metabolic; Pathway

The Carnegie Institute of Washington is awarded a grant to create a network of plant metabolism databases. At the center of the network will be PlantCyc containing pathways from many plants, supported by experimental evidence for pathways, reactions or enzymes. PlantCyc will be initialized from currently available plant metabolism databases such as AraCyc, TomatoCyc, RiceCyc, MedicagoCyc and Soybase. It will be used as a reference database (in conjunction with MetaCyc) to create multiple plant pathway genome databases (PGDBs) with substantial sequence data. To build a PGDB, putative enzyme sequences will be identified for each organism using several sequence analysis methods and Pathway Tools software will be used to generate the initial PGDBs from the annotated sequences. As each PGDB is built, all of the pathways and enzymes in the new PGDB will be validated and added to PlantCyc, and subsequently curated. Therefore, with each round of PGDB prediction, the quantity and quality of PlantCyc will be increased. The project will leverage the curation teams at other databases interested in different species as well as biochemistry experts who are interested in specific domains of metabolism in improving the content of PlantCyc and the PGDBs. All of the data will be made freely available and updates will be released on a regular basis. As the worldwide demand for production of biofuels, food, animal feed and new medicines continues to grow, there is an increasingly urgent need to develop new technologies using plants. The long-term goal of developing these technologies has prompted the sequencing of plant genomes and gene complements. There is a growing need to place the sequenced and annotated genomes in a biochemical context in order to facilitate discovery of enzymes and engineering of metabolism. This proposal will generate an infrastructure for comprehensive plant metabolism information that addresses the need to store, analyze and display the growing body of data that is emerging from both conventional biochemistry and high-throughput/large-scale data experiments. The proposed network of databases will facilitate the discovery of new enzymes and pathways, the engineering of metabolic pathways, and the curation of new findings in the context of overall metabolic scheme of an organism.

华盛顿卡内基研究所获得了建立植物代谢数据库网络的赠款。网络的中心将是植物学，其中包含许多植物的途径，并得到了途径，反应或酶的实验证据的支持。 PlantCyC将从当前可用的植物代谢数据库中初始化，例如Aracyc，Tomatocyc，Ricecyc，Medicagocyc和Soybase。它将用作参考数据库（与Metacyc结合使用），以创建具有大量序列数据的多个植物途径基因组数据库（PGDB）。为了构建PGDB，将使用多种序列分析方法和途径工具软件来确定每个生物体的推定酶序列，以从带注释的序列中生成初始PGDB。当每个PGDB构建时，新PGDB中的所有途径和酶都将得到验证并添加到PlantCyc，然后进行策划。因此，随着PGDB预测的每一轮预测，PlantCyC的数量和质量将增加。该项目将利用对不同物种感兴趣的其他数据库以及对代谢特定领域感兴趣的生物化学专家的策展人，以改善PlantCyC和PGDB的内容。所有数据将免费提供，并定期发布更新。随着全球生产生物燃料，食物，动物饲料和新药物的需求的持续增长，越来越需要使用植物开发新技术。开发这些技术的长期目标促使植物基因组和基因补充的测序。越来越需要将测序和注释的基因组放在生化环境中，以促进发现酶和代谢的工程。该提案将生成一个基础架构，以解决全面的植物代谢信息，该信息解决了从常规生物化学和高通量/大规模数据实验中浮出水面的需求。提出的数据库网络将促进新酶和途径的发现，代谢途径的工程以及在有机体的整体代谢方案的背景下的新发现的策划。