期刊
JOURNAL OF STRUCTURAL BIOLOGY
卷 161, 期 3, 页码 220-231出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.jsb.2007.10.003
关键词
electron tomography; bioinformatics; ontology; 3D reconstruction
资金
- NCRR NIH HHS [U24 RR021760, RR04050, P41 RR008605, RR08605-08S1, RR021760, P41 RR004050, RR08605] Funding Source: Medline
- NIDA NIH HHS [R01 DA016602-10, DA016602, R01 DA016602] Funding Source: Medline
- NINDS NIH HHS [R01 NS058296, R01 NS058296-01] Funding Source: Medline
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.
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