The cell centered database project: an update on building community resources for managing and sharing 3D imaging data.

Databases have become integral parts of data management, dissemination, and mining in biology. At the Second Annual Conference on Electron Tomography, held in Amsterdam in 2001, we proposed that electron tomography data should be shared in a manner analogous to structural data at the protein and sequence scales. At that time, we outlined our progress in creating a database to bring together cell level imaging data across scales, The Cell Centered Database (CCDB). The CCDB was formally launched in 2002 as an on-line repository of high-resolution 3D light and electron microscopic reconstructions of cells and subcellular structures. It contains 2D, 3D, and 4D structural and protein distribution information from confocal, multiphoton, and electron microscopy, including correlated light and electron microscopy. Many of the data sets are derived from electron tomography of cells and tissues. In the 5 years since its debut, we have moved the CCDB from a prototype to a stable resource and expanded the scope of the project to include data management and knowledge engineering. Here, we provide an update on the CCDB and how it is used by the scientific community. We also describe our work in developing additional knowledge tools, e.g., ontologies, for annotation and query of electron microscopic data.

[1]  David Lee,et al.  The Telescience Portal for advanced tomography applications , 2003, J. Parallel Distributed Comput..

[2]  Stephen T. C. Wong,et al.  Human Brain Program Research Progress in Bioinformatics/ Neuroinformatics , 2001, J. Am. Medical Informatics Assoc..

[3]  Bertram Ludäscher,et al.  A cell-centered database for electron tomographic data. , 2002, Journal of structural biology.

[4]  Mark James,et al.  Biomedical Informatics Research Network: Building a National Collaboratory to Hasten the Derivation of New Understanding and Treatment of Disease , 2005, HealthGrid.

[5]  Douglas A. Creager,et al.  The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging , 2005, Genome Biology.

[6]  Scott T. Grafton,et al.  Sharing neuroimaging studies of human cognition , 2004, Nature Neuroscience.

[7]  G A Perkins,et al.  Electron tomography of large, multicomponent biological structures. , 1997, Journal of structural biology.

[8]  V. Lučić,et al.  Structural studies by electron tomography: from cells to molecules. , 2005, Annual review of biochemistry.

[9]  K. Henrick,et al.  New electron microscopy database and deposition system. , 2002, Trends in biochemical sciences.

[10]  Maryann E Martone,et al.  Database resources for cellular electron microscopy. , 2007, Methods in cell biology.

[11]  B. Marsh,et al.  Direct continuities between cisternae at different levels of the Golgi complex in glucose-stimulated mouse islet beta cells. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Maryann E Martone,et al.  Evidence for Ectopic Neurotransmission at a Neuronal Synapse , 2005, Science.

[13]  Jack A. M. Leunissen,et al.  Evolution of web services in bioinformatics , 2005, Briefings Bioinform..

[14]  José L. V. Mejino,et al.  A reference ontology for biomedical informatics: the Foundational Model of Anatomy , 2003, J. Biomed. Informatics.

[15]  Mónica Chagoyen,et al.  Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology. , 2005, Journal of structural biology.

[16]  Li Chen,et al.  An Ontology-Driven Knowledge Environment For Subcellular Neuroanatomy , 2007, OWLED.

[17]  G. Ascoli Mobilizing the base of neuroscience data: the case of neuronal morphologies , 2006, Nature Reviews Neuroscience.

[18]  Casey H. Buitenhuys,et al.  Small Nodes of Ranvier From Peripheral Nerves of Mice Reconstructed by Electron Tomography , 2005 .

[19]  Sameer Velankar,et al.  E-MSD: improving data deposition and structure quality , 2005, Nucleic Acids Res..

[20]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[21]  Ann Zimmerman,et al.  The Biomedical Informatics Research Network , 2008 .

[22]  Amarnath Gupta,et al.  A Formal Ontology of Subcellular Neuroanatomy , 2007, Frontiers Neuroinformatics.

[23]  M. Ashburner,et al.  An ontology for cell types , 2005, Genome Biology.

[24]  Stephen H. Koslow,et al.  Celebrating a decade of neuroscience databases , 2007, Neuroinformatics.

[25]  A. Rector,et al.  Relations in biomedical ontologies , 2005, Genome Biology.

[26]  Mark H Ellisman,et al.  Ultrastructure of a Somatic Spine Mat for Nicotinic Signaling in Neurons , 2002, The Journal of Neuroscience.

[27]  Mark H. Ellisman,et al.  Differences in chloroplast ultrastructure of Phaeocystis antarctica in low and high light , 2006 .

[28]  Mark H Ellisman,et al.  Transform-based backprojection for volume reconstruction of large format electron microscope tilt series. , 2006, Journal of structural biology.