title: A cell-centered database for electron tomographic data.
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.
authors.affiliation: 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
authors.forename: Maryann E
authors.initials: ME
authors.lastname: Martone
authors.forename: Amarnath
authors.initials: A
authors.lastname: Gupta
authors.forename: Mona
authors.initials: M
authors.lastname: Wong
authors.forename: Xufei
authors.initials: X
authors.lastname: Qian
authors.forename: Gina
authors.initials: G
authors.lastname: Sosinsky
authors.forename: Bertram
authors.initials: B
authors.lastname: Ludäscher
authors.forename: Mark H
authors.initials: MH
authors.lastname: Ellisman
mesh_terms: D000818:Animals; D022082:Cellular Structures / Q000648:ultrastructure*; D016208:Databases, Factual; D001330:Electronic Data Processing; D006801:Humans; D021621:Imaging, Three-Dimensional; D008854:Microscopy, Electron; D011506:Proteins; D014057:Tomography, X-Ray Computed
chemical_list: D011506:Proteins