MongoDB for Electrophysiology Experiments

Petr Ježek, Roman Mouček, Jakub Daněk

Abstract

Many efforts are devoted to provide a unified solution for maintaining data from electrophysiological experiments. Because large data collections of heterogeneous nature are obtained, neuroinformatics databases must be robust and flexible. Current database systems are of two types. The first one uses a fixed schema while the second one is schema free. This paper discusses usage of a NoSQL database, MongoDB, for electrophysiological experiments and investigates transformation of existing electroencephalography (EEG) and event-related potentials (ERP) database records in Oracle into MongoDB. Two perspectives, flexibility and performance are discussed. A final approach that profits from combination of both concepts, is also discussed.

References

  1. Bauer, C. and King, G. (2006). Java Persistence with Hibernate. Manning, revised. edition.
  2. Carreiras, C., Silva, H., Loureno, A., and Fred, A. L. N. (2013). Storagebit - a metadata-aware, extensible, semantic and hierarchical database for biosignals. In Stacey, D., Sol-Casals, J., Fred, A. L. N., and Gamboa, H., editors, HEALTHINF, pages 65-74. SciTePress.
  3. Grewe, J., Wachtler, T., and Benda, J. (2011). A bottom-up approach to data annotation in neurophysiology. Frontiers in Neuroinformatics, 5(16).
  4. Group, I. W. (2013). Incf dataspace.
  5. Jezek, P., Stebeták, J., Bruha, P., and Moucek, R. (2013). Model of software and hardware infrastructure for electrophysiology. In Stacey, D., Solé-Casals, J., Fred, A. L. N., and Gamboa, H., editors, HEALTHINF, pages 352-356. SciTePress.
  6. Leavitt, N. (2010). Will nosql databases live up to their promise? Computer, 43(2):12-14.
  7. Pollack, M., Gierke, O., Risberg, T., Brisbin, J., and Hunger, M. (2012). Spring Data. O'Reilly Media.
  8. Rautenberg, P., Sobolev, A., Herz, A., and Wachtler, T. (2011). A database system for electrophysiological data. In Hameurlain, A., Kng, J., Wagner, R., Bhm, C., Eder, J., and Plant, C., editors, Transactions on Large-Scale Data- and Knowledge-Centered Systems IV, volume 6990 of Lecture Notes in Computer Science, pages 1-14. Springer Berlin Heidelberg.
  9. The HDF Group (2000-2010). Hierarchical data format version 5.
  10. Van Pelt, J. and van Horn, J. (2007). 1st incf workshop on sustainability of neuroscience databases. Workshop report. Stockholm.
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Paper Citation


in Harvard Style

Ježek P., Mouček R. and Daněk J. (2014). MongoDB for Electrophysiology Experiments . In Proceedings of the International Conference on Health Informatics - Volume 1: HEALTHINF, (BIOSTEC 2014) ISBN 978-989-758-010-9, pages 422-427. DOI: 10.5220/0004903604220427


in Bibtex Style

@conference{healthinf14,
author={Petr Ježek and Roman Mouček and Jakub Daněk},
title={MongoDB for Electrophysiology Experiments},
booktitle={Proceedings of the International Conference on Health Informatics - Volume 1: HEALTHINF, (BIOSTEC 2014)},
year={2014},
pages={422-427},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004903604220427},
isbn={978-989-758-010-9},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Health Informatics - Volume 1: HEALTHINF, (BIOSTEC 2014)
TI - MongoDB for Electrophysiology Experiments
SN - 978-989-758-010-9
AU - Ježek P.
AU - Mouček R.
AU - Daněk J.
PY - 2014
SP - 422
EP - 427
DO - 10.5220/0004903604220427