Dai Wei, Liang Yuyao, Zhou Z Hong
School of Health Information Sciences, University of Texas Health Science Center at Houston, 7000 Fannin, Houston, TX 77030, USA.
J Struct Biol. 2003 Oct-Nov;144(1-2):238-45. doi: 10.1016/j.jsb.2003.09.035.
The exponential increase of image data in high-resolution reconstructions by electron cryomicroscopy (cryoEM) has posed a need for efficient data management solutions in addition to powerful data processing procedures. Although relational databases and web portals are commonly used to manage sequences and structures in biological research, their application in cryoEM has been limited due to the complexity in accomplishing the dual tasks of interacting with proprietary software and simultaneously providing data access to users without database knowledge. Here, we report our results in developing web portal to SQL image databases used by the Image Management and Icosahedral Reconstruction System (IMIRS) to manage cryoEM images for subnanometer-resolution reconstructions. Fundamental issues related to the design and deployment of web portals to image databases are described. A web browser-based user interface was designed to accomplish data reporting and other database-related services, including user authentication, data entry, graph-based data mining, and various query and reporting tasks with interactive image manipulation capabilities. With an integrated web portal, IMIRS represents the first cryoEM application that incorporates both web-based data reporting tools and a complete set of data processing modules. Our examples should thus provide general guidelines applicable to other cryoEM technology development efforts.
通过电子冷冻显微镜（cryoEM）进行高分辨率重建时，图像数据呈指数级增长，这不仅需要强大的数据处理程序，还需要高效的数据管理解决方案。尽管关系数据库和门户网站通常用于管理生物学研究中的序列和结构，但由于在与专有软件交互以及在用户没有数据库知识的情况下同时提供数据访问这双重任务的复杂性，它们在冷冻电镜中的应用受到了限制。在此，我们报告了开发用于图像管理和二十面体重建系统（IMIRS）的SQL图像数据库的门户网站的成果，该系统用于管理亚纳米分辨率重建的冷冻电镜图像。描述了与图像数据库门户网站设计和部署相关的基本问题。设计了基于网络浏览器的用户界面来完成数据报告和其他与数据库相关的服务，包括用户认证、数据录入、基于图形的数据挖掘以及具有交互式图像操作功能的各种查询和报告任务。通过集成的门户网站，IMIRS代表了第一个结合基于网络的数据报告工具和一整套数据处理模块的冷冻电镜应用。因此，我们的示例应能为适用于其他冷冻电镜技术开发工作的一般指南提供参考。
