Building a Network of Plant Metabolic Pathway Databases and Communities

华盛顿的卡内基研究所获得一笔赠款，用于建立一个植物代谢数据库网络。网络的中心将是PlantCyc，它包含来自许多植物的途径，并得到途径、反应或酶的实验证据的支持。PlantCyc将从目前可用的植物代谢数据库（如AraCyc、TomatoCyc、RiceCyc、MedicagoCyc和Risbase）中初始化。它将被用作参考数据库（与MetaCyc结合），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，将使用几种序列分析方法鉴定每种微生物的推定酶序列，并使用Pathway Tools软件从注释序列生成初始PGDB。随着每个PGDB的构建，新PGDB中的所有途径和酶都将经过验证并添加到PlantCyc中，随后进行管理。因此，随着每一轮PGDB预测，PlantCyc的数量和质量都会增加。该项目将利用对不同物种感兴趣的其他数据库的策展团队以及对特定代谢领域感兴趣的生物化学专家来改善PlantCyc和PGDB的内容。所有数据都将免费提供，并定期发布更新。随着全世界对生产生物燃料、粮食、动物饲料和新药的需求不断增长，越来越迫切需要开发利用植物的新技术。开发这些技术的长期目标促进了植物基因组和基因互补序列的测序。越来越需要将测序和注释的基因组置于生物化学背景中，以促进酶的发现和代谢工程。该提案将为全面的植物代谢信息提供基础设施，以满足存储、分析和显示传统生物化学和高通量/大规模数据实验中不断增长的数据的需求。拟议的数据库网络将有助于发现新的酶和途径，代谢途径的工程，以及在生物体整体代谢方案的背景下管理新的发现。

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.