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A Holistic Approach to Testing Biomedical Hypotheses and Analysis of Biomedical Data

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Beyond Databases, Architectures and Structures. Advanced Technologies for Data Mining and Knowledge Discovery (BDAS 2015, BDAS 2016)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 613))

Abstract

Testing biomedical hypotheses is performed based on advanced and usually many-step analysis of biomedical data. This requires sophisticated analytical methods and data structures that allow to store intermediate results, which are needed in the subsequent steps. However, biomedical data, especially reference data, often change in time and new analytical methods are created every year. This causes the necessity to repeat the iterative analyses with new methods and new reference data sets, which in turn causes frequent changes of the underlying data structures. Such instability of data structures can be mitigated by the use of the idea of data lake, instead of traditional database systems.

The aim of this paper is to show system for researchers dealing with various types of biomedical data. Such a system provides a functionality of data analysis and testing different biomedical hypotheses. We treat a problem in a holistic way giving a researcher freedom in configuration his own multi-step analysis. This is possible by using a multiversion dynamic-schema data warehouse, performing parallel calculations on the virtualized computational environment, and delivering data in MapReduce-based ETL processes.

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Acknowledgments

This work was supported by The National Centre for Research and Development grant No PBS3/B3/32/2015. Presented system was developed and installed on the infrastructure of the Ziemowit computer cluster (www.ziemowit.hpc.polsl.pl) in the Laboratory of Bioinformatics and Computational Biology, The Biotechnology, Bioengineering and Bioinformatics Centre Silesian BIO-FARMA, created in the POIG.02.01.00-00-166/08 and expanded in the POIG.02.03.01-00-040/13 projects.

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Authors and Affiliations

  1. Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland

    Krzysztof Psiuk-Maksymowicz, Roman Jaksik, Sebastian Student, Damian Borys, Krzysztof Fujarewicz & Andrzej Świerniak

  2. Research and Development Department, WASKO S.A., ul. Berbeckiego 6, 44-100, Gliwice, Poland

    Aleksander Płaczek

  3. Institute of Informatics, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland

    Dariusz Mrozek

Authors
  1. Krzysztof Psiuk-Maksymowicz
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  2. Aleksander Płaczek
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  3. Roman Jaksik
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  4. Sebastian Student
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  5. Damian Borys
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  6. Dariusz Mrozek
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  7. Krzysztof Fujarewicz
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  8. Andrzej Świerniak
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Correspondence to Krzysztof Psiuk-Maksymowicz .

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Editors and Affiliations

  1. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Stanisław Kozielski

  2. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Dariusz Mrozek

  3. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Paweł Kasprowski

  4. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Bożena Małysiak-Mrozek

  5. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Daniel Kostrzewa

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Psiuk-Maksymowicz, K. et al. (2016). A Holistic Approach to Testing Biomedical Hypotheses and Analysis of Biomedical Data. In: Kozielski, S., Mrozek, D., Kasprowski, P., Małysiak-Mrozek, B., Kostrzewa, D. (eds) Beyond Databases, Architectures and Structures. Advanced Technologies for Data Mining and Knowledge Discovery. BDAS BDAS 2015 2016. Communications in Computer and Information Science, vol 613. Springer, Cham. https://doi.org/10.1007/978-3-319-34099-9_34

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  • DOI: https://doi.org/10.1007/978-3-319-34099-9_34

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-34098-2

  • Online ISBN: 978-3-319-34099-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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