A cell-centered database for electron tomographic data
A cell-centered database for electron tomographic data
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DOI：
10.1016/s1047-8477(02)00006-0
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发表时间：
2002-04-01
影响因子：
3
通讯作者：
Ellisman, MH
中科院分区：
文献类型：
--
作者：
Martone, ME;Gupta, A;Ellisman, MH
电子断层扫描为从分子到细胞的生物成分提供了丰富的三维结构数据。我们正在开发一个可访问网络的数据库，为电子断层扫描获得的高分辨率细胞水平结构和蛋白质定位数据量身定制。以细胞为中心的数据库（Cell Centered Database，简称CCDB）是使用Oracle 8i在对象关系框架上构建的，它位于加州大学圣地亚哥分校的圣地亚哥超级计算机中心的一台服务器上。数据可以通过网络界面存储和访问。每个体重建都存储有一套完整的描述符，以及倾斜图像和任何派生产品，如分割对象和动画。层析成像数据由高分辨率光显微数据补充，以提供高阶细胞和组织结构的相关数据。从重建中分割的每个对象都作为一个独特的实体包含在数据库中，并带有诸如体积、表面积、直径、长度和蛋白质标记量等测量值，从而允许查询图像特定属性。响应CCDB查询获得的数据集通过存储资源代理（Storage Resource Broker）进行检索，这是一个数据管理系统，用于透明地访问本地和分布式数据集合。CCDB旨在为结构生物学家提供资源，并使整个科学界可以使用层析成像数据集。(C) 2002 Elsevier Science （USA）。版权所有。
Electron tomography is providing a wealth of 3D structural data on biological components ranging from molecules to cells. We are developing a web-accessible database tailored to high-resolution cellular level structural and protein localization data derived from electron tomography. The Cell Centered Database or CCDB is built on an object-relational framework using Oracle 8i and is housed on a server at the San Diego Supercomputer Center at the University of California, San Diego. Data can be deposited and accessed via a web interface. Each volume reconstruction is stored with a full set of descriptors along with tilt images and any derived products such as segmented objects and animations. Tomographic data are supplemented by high-resolution light microscopic data in order to provide correlated data on higher-order cellular and tissue structure. Every object segmented from a reconstruction is included as a distinct entity in the database along with measurements such as volume, surface area, diameter, and length and amount of protein labeling, allowing the querying of image-specific attributes. Data sets obtained in response to a CCDB query are retrieved via the Storage Resource Broker, a data management system for transparent access to local and distributed data collections. The CCDB is designed to provide a resource for structural biologists and to make tomographic data sets available to the scientific community at large. (C) 2002 Elsevier Science (USA). All rights reserved.