Abstract
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.
Original language | English (US) |
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Pages (from-to) | 145-155 |
Number of pages | 11 |
Journal | Journal of Structural Biology |
Volume | 138 |
Issue number | 1-2 |
DOIs | |
State | Published - 2002 |
Externally published | Yes |
Keywords
- 3D reconstruction
- Electron tomography
- High-voltage electron microscopy
- Neuroinformatics
ASJC Scopus subject areas
- Structural Biology