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International Conference on Data Integration in the Life Sciences

DILS 2018: Data Integration in the Life Sciences pp 33–43Cite as

Construction and Visualization of Dynamic Biological Networks: Benchmarking the Neo4J Graph Database

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 11371))

Abstract

Genome analysis is a major precondition for future advances in the life sciences. The complex organization of genome data and the interactions between genomic components can often be modeled and visualized in graph structures. In this paper we propose the integration of several data sets into a graph database. We study the aptness of the database system in terms of analysis and visualization of a genome regulatory network (GRN) by running a benchmark on it. Major advantages of using a database system are the modifiability of the data set, the immediate visualization of query results as well as built-in indexing and caching features.

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Acknowledgements

Chimi Wangmo participated in the preparation of this article while visiting the University of Göttingen with a Go International Plus scholarship by the Erasmus+ Key Action of the European Commission.

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Authors and Affiliations

  1. Institute of Computer Science, University of Göttingen, Göttingen, Germany

    Lena Wiese

  2. Gyalpozhing College of Information Technology, Royal University of Bhutan, Thimphu, Bhutan

    Chimi Wangmo

  3. Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, Göttingen, Germany

    Lukas Steuernagel, Armin O. Schmitt & Mehmet Gültas

  4. Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany

    Armin O. Schmitt & Mehmet Gültas

Authors
  1. Lena Wiese
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  2. Chimi Wangmo
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  3. Lukas Steuernagel
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  4. Armin O. Schmitt
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  5. Mehmet Gültas
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Corresponding author

Correspondence to Lena Wiese .

Editor information

Editors and Affiliations

  1. TIB and Leibniz University, Hannover, Germany

    Sören Auer

  2. TIB and Leibniz University, Hannover, Germany

    Maria-Esther Vidal

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Wiese, L., Wangmo, C., Steuernagel, L., Schmitt, A.O., Gültas, M. (2019). Construction and Visualization of Dynamic Biological Networks: Benchmarking the Neo4J Graph Database. In: Auer, S., Vidal, ME. (eds) Data Integration in the Life Sciences. DILS 2018. Lecture Notes in Computer Science(), vol 11371. Springer, Cham. https://doi.org/10.1007/978-3-030-06016-9_3

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  • DOI: https://doi.org/10.1007/978-3-030-06016-9_3

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-06015-2

  • Online ISBN: 978-3-030-06016-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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