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A cell-centered database for electron tomographic data.

Maryann E Martone1, Amarnath Gupta, Mona Wong

  • 1National 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

Journal of Structural Biology
|August 6, 2002
PubMed
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The Cell Centered Database (CCDB) offers web-accessible 3D structural and protein localization data from electron tomography. This resource provides querying of image-specific attributes for structural biologists.

Area of Science:

  • Structural biology
  • Cell biology
  • Biophysics

Background:

  • Electron tomography generates extensive 3D structural data for biological components.
  • High-resolution cellular and protein localization data are crucial for understanding biological structures.
  • Existing data accessibility and querying methods for tomographic data are limited.

Purpose of the Study:

  • To develop a web-accessible database for high-resolution cellular structural and protein localization data from electron tomography.
  • To create a centralized resource for querying image-specific attributes of segmented objects.
  • To facilitate the sharing and accessibility of tomographic data within the scientific community.

Main Methods:

  • Development of the Cell Centered Database (CCDB) using an object-relational framework (Oracle 8i).

Related Experiment Videos

  • Web-based data deposition and access interface.
  • Integration of tilt images, segmented objects, animations, and associated metadata.
  • Supplementation of tomographic data with high-resolution light microscopy data.
  • Utilizing the Storage Resource Broker for data retrieval.

    • Main Results:

    • The CCDB stores detailed descriptors, tilt images, and derived products for each volume reconstruction.
    • Segmented objects are stored as distinct entities with quantitative measurements (volume, surface area, etc.) and protein labeling information.
    • The database allows querying of image-specific attributes, enabling detailed analysis of cellular structures.
    • Correlated light microscopy data provides context for higher-order cellular and tissue organization.

    Conclusions:

    • The CCDB provides a valuable, web-accessible resource for structural biologists.
    • It enhances the utility of electron tomography data by enabling detailed querying and analysis.
    • The database promotes broader access to and utilization of tomographic datasets by the scientific community.