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J Struct Biol. 2002 Apr-May;138(1-2):145-55.

A cell-centered database for electron tomographic data.

Author information

1
National Center for Microscopy and Imaging Research, Center for Research in Biological Structure and Department of Neurosciences, University of California, San Diego, La Jolla, 92093-0608, USA. mmartone@ucsd.edu

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.

PMID:
12160711
[Indexed for MEDLINE]

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