Martone Maryann E, Tran Joshua, Wong Willy W, Sargis Joy, Fong Lisa, Larson Stephen, Lamont Stephan P, Gupta Amarnath, Ellisman Mark H
Department of Neurosciences, University of California at San Diego, San Diego, CA 92093-0608, USA.
J Struct Biol. 2008 Mar;161(3):220-31. doi: 10.1016/j.jsb.2007.10.003. Epub 2007 Oct 16.
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.
数据库已成为生物学数据管理、传播和挖掘中不可或缺的一部分。在2001年于阿姆斯特丹举行的第二届电子断层扫描年度会议上，我们提议应以类似于蛋白质和序列尺度上的结构数据的方式共享电子断层扫描数据。当时，我们概述了创建一个数据库以汇集跨尺度细胞水平成像数据——细胞中心数据库（CCDB）的进展情况。CCDB于2002年正式推出，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、多光子和电子显微镜（包括相关光电子显微镜）的二维、三维和四维结构及蛋白质分布信息。许多数据集源自细胞和组织的电子断层扫描。自首次亮相后的5年里，我们已将CCDB从一个原型转变为一个稳定的资源，并扩大了项目范围，纳入了数据管理和知识工程。在此，我们提供CCDB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用于注释和查询电子显微镜数据的其他知识工具（如本体）方面的工作。
