A Microbial Biodegradation Database on the World Wide Web

万维网上的微生物生物降解数据库

• 批准号: 9630427
• 负责人: Lynda Ellis
• 金额: $ 19.64万
• 依托单位: University of Minnesota-Twin Cities
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 1996
• 资助国家: 美国
• 起止时间: 1996-08-01 至 1999-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9630427&HistoricalAwards=false
• 关键词: Microbial; Biodegradation; Database; World; Wide

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) first appeared on the World Wide Web (http://dragon.labmed.umn.edu/ ~lynda/index.html) less than one year ago to meet the information needs of microbial biotechnology. It was designed to provide information on specialized, non-intermediary metabolic pathways for the microbial biodegradation of primarily xenobiotic, organic chemical compounds. While microbial catabolism of these types of compounds in nature is more difficult to study than intermediary metabolism, it is important for understanding the cycles of nature, bioremediation of industrial chemicals, and biocatalysis for synthesizing commodity chemicals. The UM-BBD provides locally, or through external links, information on the compounds, the enzymes that metabolize them, the genes that produce the enzymes, and the organisms that contain them. In less than one year of operation, usage has grown to over 20,000 accesses a month from six continents, and over 200 national and international users have joined the UM-BBD e-mail users list. It is well accepted by its peers: Five world-renowned content experts have agreed to join the UM-BBD Scientific Advisory Board. It is or will soon be linked to by six prominent biological databases including Entrez Medline, PIR and GenBank, PUMA, Genobase and Kyoto Encyclopedia of Genes and Genomes. And it has been or will be used instructionally at the University of Minnesota, the University of Connecticut and the Hebrew University in Jerusalem. The UM-BBD's use, users and peer-acceptance within its first year of operation emphasizes a great demand for the information it contains, a design that is attractive to its users, and a desire in ~e scientific community for an accelerated pace of development. The next phase of growth includes increases in depth, breadth, quality and representations of its information; and improved tools to manipulate it; all developed in close consultation with the user community. The number of degradation pathways will be expanded from 8 to 100, the amount of information contained will increase from the present 30 to 300-500 Mbytes; and searching will be allowed not only by compound and enzyme names but by EC codes, CAS numbers, and possibly other ways including compound structure and substructure. The pathways chosen for the expansion will be chosen to represent compounds with the broadest possible set of organic functional groups and biochemical reactions. The UM-BBD will then contain direct information on the most environmentally-relevant organic molecules and a become a knowledge base that can be used to predict the metabolic and environmental fate of the majority of the 8 million known organic compounds, whose microbial metabolism has not yet been studied. The UM-BBD is well-positioned to become a community database, used and useful to scientists at every level and with a wide range of interests. A-l

明尼苏达大学生物催化/生物降解数据库（UM-BBD）首次出现在万维网（http：dragon.labmed.umn.edu/）不到一年前，以满足微生物技术的信息需求。其目的是提供关于微生物生物降解主要是生物外源性有机化合物的专门的非中间代谢途径的信息。虽然这些类型的化合物在自然界中的微生物催化比中间代谢更难研究，但它对于理解自然界的循环，工业化学品的生物修复和合成商品化学品的生物催化非常重要。UM-BBD在本地或通过外部链接提供有关化合物、代谢它们的酶、产生酶的基因以及含有它们的生物体的信息。在运作不到一年的时间里，使用率已增长到每月从六大洲访问20 000次以上，200多个国家和国际用户加入了UM-BBD电子邮件用户名单。它被同行所接受：五位世界知名的内容专家已同意加入UM-BBD科学顾问委员会。 它已经或即将与六个著名的生物学数据库相连，其中包括PIMDLINE、PIR和GenBank、CIMDA、Genobase和京都基因和基因组百科全书。它已经或将要被明尼苏达大学，康涅狄格大学和耶路撒冷的希伯来大学用于教学。UM-BBD的使用，用户和同行的认可在其第一年的操作强调了对它所包含的信息的巨大需求，对其用户有吸引力的设计，以及科学界对加速发展的渴望。下一个增长阶段包括增加其信息的深度、广度、质量和表现形式;改进操纵信息的工具;所有这些都是在与用户社区密切协商的情况下开发的。 降解途径的数量将从8个增加到100个，所包含的信息量将从目前的30兆字节增加到300-500兆字节;不仅允许通过化合物和酶名称进行搜索，还允许通过EC代码、CAS编号以及可能的其他方式（包括化合物结构和亚结构）进行搜索。选择用于扩展的途径将被选择为代表具有最广泛的有机官能团和生化反应的化合物。UM-BBD将包含与环境最相关的有机分子的直接信息，并成为一个知识库，可用于预测800万种已知有机化合物中大多数的代谢和环境命运，这些化合物的微生物代谢尚未研究。 UM-BBD很有可能成为一个社区数据库，对各个层次的科学家都很有用，而且兴趣广泛。 A-L