A Microbial Biodegradation Database on the World Wide Web

为了满足微生物生物技术的信息需求，明尼苏达大学生物催化/生物降解数据库(UM-BBD)不到一年前才首次出现在万维网(http://dragon.labmed.umn.edu/~lynda/index.html)上。它旨在提供关于主要是外来生物的有机化合物的微生物生物降解的专门的、非中间代谢途径的信息。虽然这些化合物在自然界中的微生物分解代谢比中介代谢更难研究，但它对于了解自然循环、工业化学品的生物修复以及合成商品化学品的生物催化都是重要的。UM-BBD在本地或通过外部链接提供有关化合物、代谢这些化合物的酶、产生这些酶的基因以及包含这些酶的有机体的信息。在运营不到一年的时间里，使用量增长到每月从六大洲访问超过20,000次，超过200名国内和国际用户加入了UM-BBD电子邮件用户名单。它被同行们很好地接受了：五位世界知名的内容专家已经同意加入UM-BBD科学咨询委员会。包括Entrez Medline、PIR和GenBank、PUMA、Genobase和京都基因和基因组百科全书在内的六个著名生物学数据库正在或即将与它建立联系。它已经或将在明尼苏达大学、康涅狄格大学和耶路撒冷的希伯来大学进行教学。UM-BBD在其运营的第一年内的使用、用户和同行接受度强调了对其包含的信息的巨大需求、对其用户具有吸引力的设计以及科学界对加快发展步伐的渴望。下一阶段的增长包括增加信息的深度、广度、质量和表现形式；改进处理信息的工具；所有这些都是在与用户社区密切协商的情况下制定的。降解途径的数量将从8条扩大到100条，所包含的信息量将从目前的30兆字节增加到300-500兆字节；不仅可以通过化合物和酶的名称进行搜索，还可以通过EC代码、CAS编号以及可能包括化合物结构和亚结构在内的其他方式进行搜索。为扩展选择的路径将被选择来代表具有尽可能广泛的有机官能团和生化反应的化合物。然后，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，这些有机化合物的微生物代谢尚未得到研究。UM-BBD处于有利地位，可以成为一个社区数据库，供各级和具有广泛兴趣的科学家使用和使用。A-L

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