生物数据库网络（bioDBnet）
bioDBnet: the biological database network.
作者信息
Mudunuri Uma, Che Anney, Yi Ming, Stephens Robert M
机构信息
Advanced Biomedical Computing Center, Advanced Technology Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD 21702, USA.
出版信息
Bioinformatics. 2009 Feb 15;25(4):555-6. doi: 10.1093/bioinformatics/btn654. Epub 2009 Jan 7.
Abstract
SUMMARY
bioDBnet is an online web resource that provides interconnected access to many types of biological databases. It has integrated many of the most commonly used biological databases and in its current state has 153 database identifiers (nodes) covering all aspects of biology including genes, proteins, pathways and other biological concepts. bioDBnet offers various ways to work with these databases including conversions, extensive database reports, custom navigation and has various tools to enhance the quality of the results. Importantly, the access to bioDBnet is updated regularly, providing access to the most recent releases of each individual database.
AVAILABILITY
摘要
摘要
bioDBnet是一个在线网络资源，可提供对多种类型生物数据库的互联访问。它整合了许多最常用的生物数据库，目前状态下有153个数据库标识符（节点），涵盖生物学的各个方面，包括基因、蛋白质、通路和其他生物学概念。bioDBnet提供了多种使用这些数据库的方式，包括转换、详尽的数据库报告、自定义导航，并有各种工具来提高结果质量。重要的是，对bioDBnet的访问会定期更新，可访问每个单独数据库的最新版本。
可用性
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本文引用的文献
1
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2
BioWarehouse: a bioinformatics database warehouse toolkit.生物仓库：一个生物信息学数据库仓库工具包。
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3
BIOZON: a hub of heterogeneous biological data.生物区域：一个异质生物数据的中心。
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4
Atlas - a data warehouse for integrative bioinformatics.阿特拉斯——一个用于整合生物信息学的数据仓库。
BMC Bioinformatics. 2005 Feb 21;6:34. doi: 10.1186/1471-2105-6-34.
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The generic genome browser: a building block for a model organism system database.通用基因组浏览器：模式生物系统数据库的一个构建模块。
Genome Res. 2002 Oct;12(10):1599-610. doi: 10.1101/gr.403602.
6
The human genome browser at UCSC.加州大学圣克鲁兹分校的人类基因组浏览器。
Genome Res. 2002 Jun;12(6):996-1006. doi: 10.1101/gr.229102.
7
SRS: information retrieval system for molecular biology data banks.SRS：分子生物学数据库信息检索系统。
Methods Enzymol. 1996;266:114-28. doi: 10.1016/s0076-6879(96)66010-8.
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