The Cell Centered Database project: An update on building community resources for managing and sharing 3D imaging data
The Cell Centered Database project: An update on building community resources for managing and sharing 3D imaging data
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DOI：
10.1016/j.jsb.2007.10.003
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发表时间：
2008-03-01
影响因子：
3
通讯作者：
Ellisman, Mark H.
中科院分区：
文献类型：
--
作者：
Martone, Maryann E.;Tran, Joshua;Ellisman, Mark H.
数据库已成为生物学中数据管理、传播和挖掘不可或缺的部分。2001年在阿姆斯特丹举行的第二届电子断层扫描年会上，我们提出电子断层扫描数据应以类似于蛋白质和序列层面的结构数据的方式进行共享。当时，我们概述了我们在创建一个数据库以整合跨尺度的细胞水平成像数据方面所取得的进展，即细胞中心数据库（CCDB）。细胞中心数据库于2002年正式启动，作为细胞和亚细胞结构的高分辨率三维光学和电子显微镜重建的在线存储库。它包含来自共聚焦显微镜、多光子显微镜和电子显微镜的二维、三维和四维结构及蛋白质分布信息，包括相关的光学和电子显微镜信息。许多数据集来自细胞和组织的电子断层扫描。自其首次推出以来的5年里，我们已将细胞中心数据库从一个原型转变为一个稳定的资源，并扩大了项目的范围，使其包括数据管理和知识工程。在此，我们提供关于细胞中心数据库的最新情况以及科学界如何使用它。我们还描述了我们在开发其他知识工具（例如本体论）以用于电子显微镜数据的注释和查询方面所做的工作。（C）2007爱思唯尔公司。保留所有权利。
Databases have become integral parts of data management, dissemination, and mining in biology. At the Second Annual Conference on Electron Tomography, held in Amsterdam in 2001, we proposed that electron tomography data should be shared in a manner analogous to structural data at the protein and sequence scales. At that time, we outlined our progress in creating a database to bring together cell level imaging data across scales, The Cell Centered Database (CCDB). The CCDB was formally launched in 2002 as an on-line repository of high-resolution 3D light and electron microscopic reconstructions of cells and subcellular structures. It contains 2D, 3D, and 4D structural and protein distribution information from confocal, multiphoton, and electron microscopy, including correlated light and electron microscopy. Many of the data sets are derived from electron tomography of cells and tissues. In the 5 years since its debut, we have moved the CCDB from a prototype to a stable resource and expanded the scope of the project to include data management and knowledge engineering. Here, we provide an update on the CCDB and how it is used by the scientific community. We also describe our work in developing additional knowledge tools, e.g., ontologies, for annotation and query of electron microscopic data. (C) 2007 Elsevier Inc. All rights reserved.