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Object Oriented Database and Electronic Notebook for Transmission Electron Microscopy

Published online by Cambridge University Press:  21 November 2003

Steven J. Ludtke
Affiliation:
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Laurie Nason
Affiliation:
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Haili Tu
Affiliation:
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Liwei Peng
Affiliation:
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Wah Chiu
Affiliation:
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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Abstract

As high-resolution biological transmission electron microscopy (TEM) has increased in popularity over recent years, the volume of data and number of projects underway has risen dramatically. A robust tool for effective data management is essential to efficiently process large data sets and extract maximum information from the available data. We present the Electron Microscopy Electronic Notebook (EMEN), a portable, object-oriented, web-based tool for TEM data archival and project management. EMEN has several unique features. First, the database is logically organized and annotated so multiple collaborators at different geographical locations can easily access and interpret the data without assistance. Second, the database was designed to provide flexibility to the user, so it can be used much as a lab notebook would be, while maintaining a structure suitable for data mining and direct interaction with data-processing software. Finally, as an object-oriented database, the database structure is dynamic and can be easily extended to incorporate information not defined in the original database specification.

Type
Microscopy Techniques
Copyright
© 2003 Microscopy Society of America

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References

REFERENCES

Carazo, J.M. & Stelzer, E.H. (1999). The BioImage Database Project: Organizing multidimensional biological images in an object-relational database. J Struct Biol 125, 97102.Google Scholar
Fellmann, D., Pulokas, J., Milligan, R.A., Carragher, B., & Potter, C.S. (2002). A relational database for cryoEM: Experience at one year and 50 000 images. J Struct Biol 137, 273282.Google Scholar
Kalko, S.G., Chagoyen, M., Jimenez-Lozano, N., Verdaguer, N., Fita, I., & Carazo, J.M. (2000). The need for a shared database infrastructure: Combining X-ray crystallography and electron microscopy. Eur Biophys J 29, 457462.Google Scholar
Liang, Y., Ke, E.Y., & Zhou, Z.H. (2002). IMIRS: A high-resolution 3D reconstruction package integrated with a relational image database. J Struct Biol 137, 292304.Google Scholar
Lindek, S., Fritsch, R., Machtynger, J., de Alarcon, P.A., & Chagoyen, M. (1999). Design and realization of an on-line database for multidimensional microscopic images of biological specimens. J Struct Biol 125, 103111.CrossRefGoogle Scholar
Ludtke, S.J., Baldwin, P.R., & Chiu, W. (1999). EMAN: Semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 128, 8297.Google Scholar
Martone, M.E., Gupta, A., Wong, M., Qian, X., Sosinsky, G., Ludascher, B., & Ellisman, M.H. (2002). A cell-centered database for electron tomographic data. J Struct Biol 138, 145155.Google Scholar
Metoz, F., Sherman, M.B., & Schmid, M.F. (2001). Adopting a database as a solution to managing electron image data. J Struct Biol 133, 170175.Google Scholar