The University of Minnesota Biocatalysis/Biodegradation Database: Post-genomic data mining
The University of Minnesota Biocatalysis/Biodegradation Database: Post-genomic data mining
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DOI：
10.1093/nar/gkg048
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发表时间：
2003-01-01
影响因子：
14.9
通讯作者：
Wackett, LP
中科院分区：
文献类型：
--
作者：
Ellis, LBM;Hou, BK;Wackett, LP
明尼苏达大学生物催化/生物降解数据库(UM-BBD，http://umbbd.ahc.umn.edu/))提供有关微生物分解代谢和相关生物转化的精选信息，主要针对环境污染物。目前，它包含130多条代谢途径、800个反应、750种化合物和500种酶的信息。在过去两年里，它增加了力度，列入了更多金属和类金属微生物新陈代谢的例子；并扩大了所包括的信息类型，以包含许多化学元素的微生物生物转化和与之结合的相互作用。它还增加了访问(挖掘)这些数据的方式。增加了基于结构的搜索，用于精确匹配、相似性或者说子结构。对UM-BBD反应的分析已经导致了一个原型、引导的路径预测系统。引导式预测是指在每一步向用户展示所有可能的生物转化，并引导整个过程得出结论。挖掘UM-BBD的数据为微生物世界如何回收有机官能团提供了独特的视角。我们鼓励BBD用户对数据库的方方面面发表评论，包括其中包含的信息和可以挖掘这些信息的工具。数据库和预测系统是在科学界的指导下开发的。
The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolism and related biotransformations, primarily for environmental pollutants. Currently, it contains information on over 130 metabolic pathways, 800 reactions, 750 compounds and 500 enzymes. In the past two years, it has increased its breath to include more examples of microbial metabolism of metals and metalloids; and expanded the types of information it includes to contain microbial biotransformations of, and binding interactions with many chemical elements. It has also increased the ways in which this data can be accessed (mined). Structure-based searching was added, for exact matches, similarity, or substructures. Analysis of UM-BBD reactions has lead to a prototype, guided, pathway prediction system. Guided prediction means that the user is shown all possible biotransformations at each step and guides the process to its conclusion. Mining the UM-BBD's data provides a unique view into how the microbial world recycles organic functional groups. UM-BBD users are encouraged to comment on all aspects of the database, including the information it contains and the tools by which it can be mined. The database and prediction system develop under the direction of the scientific community.