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Processing Neurology Clinical Data for Knowledge Discovery: Scalable Data Flows Using Distributed Computing

  • Satya S. SahooEmail author
  • Annan Wei
  • Curtis Tatsuoka
  • Kaushik Ghosh
  • Samden D. Lhatoo
Chapter
  • 3.7k Downloads
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9605)

Abstract

The rapidly increasing capabilities of neurotechnologies are generating massive volumes of complex multi-modal data at a rapid pace. This neurological big data can be leveraged to provide new insights into complex neurological disorders using data mining and knowledge discovery techniques. For example, electrophysiological signal data consisting of electroencephalogram (EEG) and electrocardiogram (ECG) can be analyzed for brain connectivity research, physiological associations to neural activity, diagnosis, and care of patients with epilepsy. However, existing approaches to store and model electrophysiological signal data has several limitations, which make it difficult for signal data to be used directly in data analysis, signal visualization tools, and knowledge discovery applications. Therefore, use of neurological big data for secondary analysis and potential development of personalized treatment strategies requires scalable data processing platforms. In this chapter, we describe the development of a high performance data flow system called Signal Data Cloud (SDC) to pre-process large-scale electrophysiological signal data using open source Apache Pig. The features of this neurological big data processing system are: (a) efficient partitioningof signal data into fixed size segments for easier storage in high performance distributed file system, (b) integration and semantic annotation of clinical metadata using an epilepsy domain ontology, and (c) transformation of raw signal data into an appropriate format for use in signal analysis platforms. In this chapter, we also discuss the various challenges being faced by the biomedical informatics community in the context of Big Data, especially the increasing need to ensure data quality and scientific reproducibility.

Keywords

Electrophysiological signal data Epileptic seizure networks Neurology Clinical research Apache pig Distributed computing 

Notes

Acknowledgements

This work is supported in part by the National Institutes of Biomedical Imaging and Bioengineering (NIBIB) Big Data to Knowledge (BD2 K) grant (1U01EB020955) and the National Institutes of Neurological Disorders and Stroke (NINDS) Center for SUDEP Research grant (1U01NS090407-01).

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Copyright information

© Springer International Publishing AG 2016

Authors and Affiliations

  • Satya S. Sahoo
    • 1
    • 2
    Email author
  • Annan Wei
    • 2
  • Curtis Tatsuoka
    • 3
  • Kaushik Ghosh
    • 4
  • Samden D. Lhatoo
    • 3
  1. 1.Division of Medical Informatics, Department of Epidemiology and Biostatistics, School of MedicineCase Western Reserve UniversityClevelandUSA
  2. 2.Department of Electrical Engineering and Computer Science, School of EngineeringCase Western Reserve UniversityClevelandUSA
  3. 3.Department of Neurology, Epilepsy CenterUniversity Hospitals Case Medical CenterClevelandUSA
  4. 4.Department of Mathematical SciencesUniversity of NevadaLas VegasUSA

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