The Cell-Centered Database: A Database for Multiscale Structural and Protein Localization Data from Light and Electron Microscopy

Abstract

The creation of structured shared data repositories for molecular data in the form of web-accessible databases like GenBank has been a driving force behind the genomic revolution. These resources serve not only to organize and manage molecular data being created by researchers around the globe, but also provide the starting point for data mining operations to uncover interesting information present in the large amount of sequence and structural data. To realize the full impact of the genomic and proteomic efforts of the last decade, similar resources are needed for structural and biochemical complexity in biological systems beyond the molecular level, where proteins and macromolecular complexes are situated within their cellular and tissue environments. In this review, we discuss our efforts in the development of neuroinformatics resources for managing and mining cell level imaging data derived from light and electron microscopy. We describe the main features of our web-accessible database, the Cell Centered Database (CCDB; http://ncmir.ucsd.edu/CCDB/), designed for structural and protein localization information at scales ranging from large expanses of tissue to cellular microdomains with their associated macromolecular constituents. The CCDB was created to make 3D microscopic imaging data available to the scientific community and to serve as a resource for investigating structural and macromolecular complexity of cells and tissues, particularly in the rodent nervous system.

The combination of chemical fixation procedures with high pressure freezing and freeze substitution preserves highly labile tissue ultrastructure for electron tomography applications

“…data and reconstructions as well as animations of the volumes are available upon publication in the Cell Centered Database (CCDB) Martone et al, 2003). The accession numbers for these data sets are: 3649 (tomogram displayed in Fig.…”

Stepping into the Third Dimension

“…Efforts to facilitate the sharing of primary data in the neuroscience community are now under development (Martone et al, 2004). For example, the Cell Centered Database (Martone et al, 2003) (http://ccdb.ucsd.edu) at the National Center for Microscopy and Imaging Research aims to make unique and valuable datasets (2D, 3D, and 4D data from light and electron microscopy) available to the scientific community for visualization, reuse, and reanalysis. Similar efforts by the European Bioinformatics Institute with EMDep database address the problem of storing and sharing 3D EM data.…”

Provenance in neuroimaging

“…Some data provenance is typically captured at the site where the data is collected, in the headers of image files or in databases that record image acquisition (Erberich et al, 2007;Martone et al, 2003). An abbreviated form of this kind of provenance is often reported in method descriptions or even in the image files themselves (Bidgood et al, 1997).…”