Gardiner-Garden M, Littlejohn T G
Entigen Pty Ltd, Eveleigh NSW, Australia.
Brief Bioinform. 2001 May;2(2):143-58. doi: 10.1093/bib/2.2.143.
Microarray technology has become one of the most important functional genomics technologies. A proliferation of microarray databases has resulted. It can be difficult for researchers exploring this technology to know which bioinformatics systems best meet their requirements. In order to obtain a better understanding of the available systems, a survey and comparative analysis of microarray databases was undertaken. The survey included databases that are currently available, as well as databases that should become available in early 2001. Databases fall into three categories: (i) those that can be installed locally, (ii) those available for public data submission and (iii) those available for public query. Developers of microarray gene-expression databases were asked questions regarding the scope and availability of their database, its system requirements, its future compliance with MGED (Microarray Gene Expression Database) standards, and its associated analytical tools. Participants included AMAD (Stanford/Berkeley/UCSF), ArrayExpress (EBI), ChipDB (MIT/Whitehead), GeneX (NCGR), GeNet (Silicon Genetics), GeneDirector (BioDiscovery), GEO (NCBI), GXD (Jackson Laboratory), mAdb (NCI), maxdSQL (University of Manchester), NOMAD (UCSF), RAD (University of Pennsylvania) and SMD (Stanford University). Other database developers were contacted but data was not available at the time of manuscript preparation. Each database fulfils a different role, reflecting the widely varying needs of microarray users.
微阵列技术已成为最重要的功能基因组学技术之一。随之产生了大量的微阵列数据库。探索这项技术的研究人员可能很难知道哪些生物信息学系统最符合他们的需求。为了更好地了解现有的系统，我们对微阵列数据库进行了调查和比较分析。该调查包括当前可用的数据库，以及预计在2001年初可用的数据库。数据库分为三类：(i) 可在本地安装的数据库；(ii) 可供公众提交数据的数据库；(iii) 可供公众查询的数据库。我们向微阵列基因表达数据库的开发者询问了有关其数据库的范围和可用性、系统要求、未来是否符合MGED（微阵列基因表达数据库）标准以及其相关分析工具等问题。参与调查的包括AMAD（斯坦福大学/伯克利分校/加州大学旧金山分校）、ArrayExpress（欧洲生物信息学研究所）、ChipDB（麻省理工学院/怀特黑德研究所）、GeneX（国家基因组资源中心）、GeNet（硅基因公司）、GeneDirector（生物发现公司）、GEO（美国国立医学图书馆国家生物技术信息中心）、GXD（杰克逊实验室）、mAdb（美国国立癌症研究所）、maxdSQL（曼彻斯特大学）、NOMAD（加州大学旧金山分校）、RAD（宾夕法尼亚大学）和SMD（斯坦福大学）。我们还联系了其他数据库开发者，但在撰写本文时未能获取相关数据。每个数据库都发挥着不同的作用，反映了微阵列用户广泛多样的需求。
