title: 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.
authors.affiliation: Department of Neurosciences, University of California at San Diego, San Diego, CA, USA. mmartone@ucsd.edu
authors.forename: Maryann E
authors.initials: ME
authors.lastname: Martone
authors.forename: Shenglan
authors.initials: S
authors.lastname: Zhang
authors.forename: Amarnath
authors.initials: A
authors.lastname: Gupta
authors.forename: Xufei
authors.initials: X
authors.lastname: Qian
authors.forename: Haiyun
authors.initials: H
authors.lastname: He
authors.forename: Diana L
authors.initials: DL
authors.lastname: Price
authors.forename: Mona
authors.initials: M
authors.lastname: Wong
authors.forename: Simone
authors.initials: S
authors.lastname: Santini
authors.forename: Mark H
authors.initials: MH
authors.lastname: Ellisman
mesh_terms: D001921:Brain; D001931:Brain Mapping; D022082:Cellular Structures / Q000378:metabolism*; D019295:Computational Biology; D016208:Databases, Factual; D007091:Image Processing, Computer-Assisted / Q000379:methods; D016247:Information Storage and Retrieval; D020407:Internet; D008853:Microscopy / Q000379:methods; D008854:Microscopy, Electron; D009317:National Library of Medicine (U.S.); D009862:Online Systems / Q000458:organization & administration; D011506:Proteins / Q000378:metabolism*; D014481:United States; D000078329:Workforce
chemical_list: D011506:Proteins