research-article

Benchmarking a distributed database design that supports patient cohort identification

Authors:

Jero Mario Schäfer,

Lena WieseAuthors Info & Claims

IDEAS '20: Proceedings of the 24th Symposium on International Database Engineering & Applications

Article No.: 18, Pages 1 - 8

https://doi.org/10.1145/3410566.3410608

Published: 25 August 2020 Publication History

Abstract

In this article we present the implementation and benchmarking of a medical information system on top of a distributed relational database system. We enhanced a distributed database system with the implementation of a clustering (based on similarity of disease terms) that induces a primary horizontal fragmentation of a data table and derived fragmentations of secondary tables. With our clustering-based fragmentation, data locality for similarity-based query answering is ensured so that data do not have to be sent unnecessarily over the network. In our benchmark we show that we achieve a significant efficiency gain when retrieving all relevant related answers.

References

[1]

S. Gombar, A. Callahan, R. Califf, R. Harrington, and N. H. Shah. It is time to learn from patients like mine. npj Digital Medicine, 2(1):1--3, 2019.

[2]

T. F. Gonzalez. Clustering to minimize the maximum intercluster distance. Theoretical Computer Science, 38:293 -- 306, 1985.

[3]

K. Inoue and L. Wiese. Generalizing conjunctive queries for informative answers. In International Conference on Flexible Query Answering Systems, pages 1--12. Springer, 2011.

Digital Library

[4]

A. E. Johnson, T. J. Pollard, L. Shen, H. L. Li-Wei, M. Feng, M. Ghassemi, B. Moody, P. Szolovits, L. A. Celi, and R. G. Mark. MIMIC-III, a freely accessible critical care database. Scientific data, 3(1):1--9, 2016.

[5]

V. Kantere. Query similarity for approximate query answering. In International Conference on Database and Expert Systems Applications, pages 355--367. Springer, 2016.

[6]

Y. Lu, A. Shanbhag, A. Jindal, and S. Madden. Adaptdb: adaptive partitioning for distributed joins. Proceedings of the VLDB Endowment, 10(5):589--600, 2017.

Digital Library

[7]

D. Martinenghi and R. Torlone. Taxonomy-based relaxation of query answering in relational databases. The VLDB Journal, 23(5):747--769, 2014.

Digital Library

[8]

S. Murphy and A. Wilcox. Mission and sustainability of informatics for integrating biology and the bedside (i2b2). eGEMs, 2(2), 2014.

[9]

National Library of Medicine. Medical subject headings, Nov 2019.

[10]

S. Navathe, S. Ceri, G. Wiederhold, and J. Dou. Vertical partitioning algorithms for database design. ACM Transactions on Database Systems (TODS), 9(4):680--710, 1984.

[11]

M. T. Özsu and P. Valduriez. Principles of Distributed Database Systems. Prentice-Hall, Inc., Upper Saddle River, NJ, USA, 1991.

[12]

A. Poulovassilis. Applications of flexible querying to graph data. In Graph Data Management, Data-Centric Systems and Applications, pages 97--142. Springer, 2018.

[13]

K. Tan. Distributed database systems. In Encyclopedia of Database Systems (2nd ed.). Springer, 2018.

[14]

A. Tashkandi, I. Wiese, and L. Wiese. Efficient in-database patient similarity analysis for personalized medical decision support systems. Big data research, 13:52--64, 2018.

[15]

I. Wiese, N. Sarna, L. Wiese, A. Tashkandi, and U. Sax. Concept acquisition and improved in-database similarity analysis for medical data. Distributed and Parallel Databases, pages 1--25, 2018.

[16]

L. Wiese. Advanced Data Management for SQL, NoSQL, Cloud and Distributed Databases. DeGruyter/Oldenbourg, 2015.

[17]

L. Wiese, A. O. Schmitt, and M. Gültas. Big data technologies for DNA sequencing. In Encyclopedia of Big Data Technologies. Springer, 2019.

[18]

E. Zamanian, C. Binnig, and A. Salama. Locality-aware partitioning in parallel database systems. In Proceedings of the 2015 ACM SIGMOD International Conference on Management of Data, pages 17--30, 2015.

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Cited By

Kumar SDash KPiduru BRajkumar KBhaskar BTiwari M(2023)Security and Privacy Challenges in Distributed Database Management Systems2023 Global Conference on Information Technologies and Communications (GCITC)10.1109/GCITC60406.2023.10426303(1-6)Online publication date: 1-Dec-2023
https://doi.org/10.1109/GCITC60406.2023.10426303
Pandat AGupta NBhise M(2021)Load Balanced Semantic Aware Distributed RDF GraphProceedings of the 25th International Database Engineering & Applications Symposium10.1145/3472163.3472167(127-133)Online publication date: 14-Jul-2021
https://dl.acm.org/doi/10.1145/3472163.3472167

Index Terms

Benchmarking a distributed database design that supports patient cohort identification
1. Information systems
  1. Data management systems
    1. Database management system engines
      1. Database query processing
        Query optimization
      2. Parallel and distributed DBMSs
        Relational parallel and distributed DBMSs

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cover image ACM Other conferences

IDEAS '20: Proceedings of the 24th Symposium on International Database Engineering & Applications

August 2020

252 pages

ISBN:9781450375030

DOI:10.1145/3410566

General Chairs:
Bipin C. Desai
Concordia University, Canada
,
Wan-Sup Cho
Chungbuk National University, Korea

Copyright © 2020 ACM.

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 25 August 2020

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Fraunhofer

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IDEAS 2020

IDEAS 2020: 24th International Database Engineering & Applications Symposium

August 12 - 14, 2020

Seoul, Republic of Korea

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IDEAS '20 Paper Acceptance Rate 27 of 57 submissions, 47%;

Overall Acceptance Rate 74 of 210 submissions, 35%

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Cited By

Kumar SDash KPiduru BRajkumar KBhaskar BTiwari M(2023)Security and Privacy Challenges in Distributed Database Management Systems2023 Global Conference on Information Technologies and Communications (GCITC)10.1109/GCITC60406.2023.10426303(1-6)Online publication date: 1-Dec-2023
https://doi.org/10.1109/GCITC60406.2023.10426303
Pandat AGupta NBhise M(2021)Load Balanced Semantic Aware Distributed RDF GraphProceedings of the 25th International Database Engineering & Applications Symposium10.1145/3472163.3472167(127-133)Online publication date: 14-Jul-2021
https://dl.acm.org/doi/10.1145/3472163.3472167

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