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

Neuroinformatics

Volumn 1, Issue 4, 2003, Pages 379-395

  Martone, Maryann E ^a   Zhang, Shenglan ^a   Gupta, Amarnath ^b   Qian, Xufei ^b   He, Haiyun ^c   Price, Diana L ^a   Wong, Mona ^a   Santini, Simone ^c   Ellisman, Mark H ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Biomedical Informatics Research Network (BIRN); Confocal microscopy; Electron tomography; High voltage electron microscopy

Indexed keywords

GENE PRODUCT;

BIOINFORMATICS; BRAIN CORTEX; CONFOCAL MICROSCOPY; DATA BASE; ELECTRON MICROSCOPY; GENOMICS; INTERNET; MICROSCOPY; NERVE CELL; NEUROANATOMY; NONHUMAN; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PURKINJE CELL; RAT; RESEARCH; REVIEW; THREE DIMENSIONAL IMAGING; TOMOGRAPHY;

BRAIN; BRAIN MAPPING; CELLULAR STRUCTURES; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; IMAGE PROCESSING, COMPUTER-ASSISTED; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MICROSCOPY; MICROSCOPY, ELECTRON; NATIONAL LIBRARY OF MEDICINE (U.S.); ONLINE SYSTEMS; PROTEINS; UNITED STATES;

EID: 0242321783     PISSN: 15392791     EISSN: None     Source Type: Journal    
DOI: 10.1385/NI:1:4:379     Document Type: Review

References (42)

1. Baldock, R. A., Bard, J. B. L., Burger, A., et al. (2003) EMAP and EMAGE: A framework for understanding spatially organized data. Neuroinformatics 1, 309-326
2. Baxevanis, A. D. (2003) The Molecular Biology Database Collection: 2003 update. Nucleic Acids Res. 31, 1-12
3. Berman, H. M., Westbrook, J., Feng, Z., et al. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
4. Bjaalie, J. G. (2002) Opinion: Localization in the brain: new solutions emerging. Nat. Rev. Neurosci. 3, 322-325.
5. Bohm, J., Frangakis, A. S., Hegerl, R., Nickell, S., Typke, D., and Baumeister, W. (2000) From the cover: toward detecting and identifying macromolecules in a cellular context: template matching applied to electron tomograms. Proc. Natl. Acad. Sci. U. S. A. 97, 14245-14250.
6. Boutselakis, H., Dimitropoulos, D., Fillon, J., et al. (2003) E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res. 31, 458-462.
7. Bowden, D. M. and Dubach, M. F. (2003) NeuroNames 2002. Neuroinformatics 1, 43-59.
8. Brevik, A., Leergaard, T. B., Svanevik, M., and Bjaalie, J. G. (2001) Three-dimensional computerised atlas of the rat brain stem precerebellar system: approaches for mapping, visualization, and comparison of spatial distribution data. Anat. Embryol. (Berl) 204, 319-332.
9. Capani, F., Martone, M. E., Deerinck, T. J., and Ellisman, M. H. (2001) Selective localization of high concentrations of F-actin in subpopulations of dendritic spines in rat central nervous system: a three-dimensional electron microscopic study. J. Comp. Neurol. 435, 156-170.
10. Fox, P. T. and Lancaster, J. L. (2002) Opinion: Mapping context and content: the BrainMap model. Nat. Rev. Neurosci. 3, 319-321.
11. Frank, J., Wagenknecht, T., McEwen, B. F., Marko, M., Hsieh, C. E., and Manella, C. A. (2002) Three-dimensional imaging of biological complexity. J. Struct. Biol. 138, 85-91.
12. Gaietta, G., Deerinck, T. J., Adams, S. R., et al. (2002) Multicolor and electron microscopic imaging of connexin trafficking. Science 296, 503-507.
13. Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nature Genetics 25, 25-29.
14. Gupta, A., Ludaescher, B., and Martone, M. E. (2000) Knowledge-Based Integration of Neuroscience Data Sources. Proceedings of the 12th International Conference on Scientific and Statistical Database Management (SSDBM'00) IEEE Computer Society.
15. Harlow, M. L., Ress, D., Stoschek, A., Marshall, R. M., and McMahan, U. J. (2001) The architecture of active zone material at the frog's neuromuscular junction. Nature 409, 479-484.
16. Hessler, D., Young, S. J., Carragher, B. O., et al. (1992) Programs for visualization in three-dimensional microscopy. Neuroimage 1, 55-67.
17. Hole, W. T. and Srinivasan, S. (2002) Adding NeuroNames to the UMLS metathesaurus. Neuroinformatics 1, 61-63.
18. Kotter, R. (2001) Neuroscience databases: tools for exploring brain structure-function relationships. Philos. Trans. R Soc. Lond. B. Biol. Sci. 356, 1111-1120.
19. Kremer, J. R., Mastronarde, D. N., and McIntosh, J. R. (1996) Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71-76.
20. Kumar, A., Cheung, K. H., Tosches, N., et al. (2002) The TRIPLES database: a community resource for yeast molecular biology. Nucleic Acids Res. 30, 73-75.
21. Ludäscher, B., Gupta, A., and Martone, M. E. (2001) Model-based mediation with domain maps. Proceedings of the 17th International Conference on Data Engineering, IEEE Computer Society 2001, Heidelberg, Germany.
22. MacKenzie-Graham, A., Jones, E. S., Shattuck, D. W., Dinov, I., Bota, M., and Toga, A. W. (2003) The informatics of a C57BL/6 mouse brain atlas. Neuroinformatics 1, 397-410.
23. Martone, M. E., Alba, S. A., Edelman, V. M., Airey, J. A., and Ellisman, M. H. (1997) Distribution of inositol-1,4,5-trisphosphate and ryanodine receptors in rat neostriatum. Brain Res. 756, 9-21.
24. Martone, M. E., Deerinck, T. J., Yamada, N., Bushong, E., and Ellisman, M. H. (2000) Correlated 3D light and electron microscopy: use of high voltage electron microscopy and electron tomography for imaging large biological structures. J. Histotechnology 23, 261-270.
25. Martone, M. E., Gupta, A., Ludascher, B., Zaslavsky, I., and Ellisman, M. H. (2002a) Federation of brain data using knowledge guided mediation, in Neuroscience databases: a practical guide, R. Kotter, Knopf, New York, pp. 275-292.
26. Martone, M. E., Gupta, A., Wong, M., et al. (2002b) A cell-centered database for electron tomographic data. J. Struct. Biol. 138, 145-155.
27. Martone, M. E., Jones, Y. Z., Young, S. J., Ellisman, M. H., Zivin, J. A., and Hu B. R. (1999) Modification of postsynaptic densities after transient cerebral ischemia: a quantitative and three-dimensional ultrastructural study. J. Neurosci. 19, 1988-1997.
28. Medalia, O., Weber, I., Frangakis, A., Nicastro, D., Gerisch, G., and Baumeister, W. (2002) Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 298, 1209-1213.
29. Ortiz De Solorzano, C., Costes, S., Callahan, D. E., Parvin, B., and Barcellos-Hoff, M. H. (2002) Applications of quantitative digital image analysis to breast cancer research. Microsc. Res. Tech. 59, 119-127.
30. Paxinos, G. and Franklin, K. B. J. (2000) The mouse brain is stereotaxic coordinates. San Diego, Academic Press. Paxinos, G. and Watson, C. (1998) The rat brain in stereotaxic coordinates. San Diego, Academic Press.
31. Paxinos, G. and Franklin, K. B. J. (2000) The mouse brain is stereotaxic coordinates. San Diego, Academic Press. Paxinos, G. and Watson, C. (1998) The rat brain in stereotaxic coordinates. San Diego, Academic Press.
32. Perkins, G., Renken, C., Martone, M. E., Young, S. J., Ellisman, M., and Frey T. (1997a) Electron tomography of neuronal mitochondria: three-dimensional structure and organization of cristae and membrane contacts. J. Struct. Biol. 119, 260-272.
33. Perkins, G. A., Renken, C. W., Song, J. Y., et al (1997b) Electron tomography of large, multicomponent biological structures. J. Struct. Biol. 120, 219-27.
34. Rosen, G. D., La Porte, N.T., Diechtiareff, B., et al. (2003) Informatics center for mouse genomics: the dissection of complex traits of the nervous system. Neuroinformatics 1, 327-342
35. Shepherd, G. M., Mirsky, J. S., Healy, M. D., et al. (1998) The Human Brain Project: neuroinformatics tools for integrating, searching and modeling multidisciplinary neuroscience data. Trends Neurosci. 21, 460-468.
36. Shotton, D. M. (2000) From image to knowledge: the state of the art in image bioinformatics. Microscopy and Analysis 45, 15-17.
37. Sinha, U., Bui, A., Taira, R., et al. (2002) A review of medical imaging informatics. Ann. N. Y. Acad. Sci. 980, 168-197.
38. Swedlow, J. R., Goldberg, I., Brauner, E., and Sorger, P. K. (2003) Informatics and quantitative analysis in biological imaging. Science 300, 100-102.
39. Toga, A. (2002) Neuroimage databases: the good, the bad, and the ugly. Nat. Rev. Neurosci. 3, 302-308.
40. Van Essen, D. C., Drury, H. A., Dickson, J., Harwell, J., Hanlon, D., and Anderson, C. H. (2001) An integrated software suite for surface-based analyses of cerebral cortex. J. Am. Med. Inform. Assoc. 8, 443-459.
41. Wilson, C. J., Mastronarde, D. N., McEwen, B., and Frank, J. (1992) Measurement of neuronal surface area using high-voltage electron microscope tomography. Neuroimage 1, 11-22.
42. Zhang, S., Qian, X., Gupta, A., Martone, M. E. (2003) A Practical Approach for Microscopy Imaging Data Management (MIDM) in Neuroscience. 15th International Conference on Scientific and Statistical Database Management (SSDBM 2003) July 9-11 Cambridge, MA, in press.