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. 2007 Jan-Feb;14(1):86-93.
doi: 10.1197/jamia.M2189. Epub 2006 Oct 26.

Dynamic tables: an architecture for managing evolving, heterogeneous biomedical data in relational database management systems

John Corwin  1 , Avi Silberschatz, Perry L Miller, Luis Marenco
Affiliations

Dynamic tables: an architecture for managing evolving, heterogeneous biomedical data in relational database management systems

John Corwin et al. J Am Med Inform Assoc. 2007 Jan-Feb.

Abstract

Data sparsity and schema evolution issues affecting clinical informatics and bioinformatics communities have led to the adoption of vertical or object-attribute-value-based database schemas to overcome limitations posed when using conventional relational database technology. This paper explores these issues and discusses why biomedical data are difficult to model using conventional relational techniques. The authors propose a solution to these obstacles based on a relational database engine using a sparse, column-store architecture. The authors provide benchmarks comparing the performance of queries and schema-modification operations using three different strategies: (1) the standard conventional relational design; (2) past approaches used by biomedical informatics researchers; and (3) their sparse, column-store architecture. The performance results show that their architecture is a promising technique for storing and processing many types of data that are not handled well by the other two semantic data models.

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Figures

Figure 1
Figure 1
A typical query in the SenseLab database expressed using horizontal and vertical data representations.
Figure 2
Figure 2
Horizontal, vertical, and decomposed storage models.
Figure 3
Figure 3
Action performed when updating attribute a to a’ on a dynamic table.
Figure 4
Figure 4
A good opportunity for projection pushing.
Figure 5
Figure 5
A candidate for conditional select optimization.
Figure 6
Figure 6
Comparison of query execution time for an attribute-centered query on SenseLab data without indexes.
Figure 7
Figure 7
Comparison of query execution time for an attribute-centered query on SenseLab data with indexes on queried attributes.
Figure 8
Figure 8
SQL queries to alter the type of a column representing the year of publication of a paper from a string value to an integer value.
Figure 9
Figure 9
Comparison of query execution time for an attribute-centered query on TrialDB data with indexes on queried attributes.
Figure 10
Figure 10
Comparison of query execution time for an entity-centered query on TrialDB data.
See this image and copyright information in PMC

References

    1. Nadkarni PM, Brandt C, Frawley S, et al. Managing attribute-value clinical trials data using the ACT/DB client-server database system J Am Med Inform Assoc 1998;5:139-151. - PMC - PubMed
    1. Miller PL, Nadkarni P, Singer M, Marenco L, Hines M, Shepherd G. Integration of multidisciplinary sensory data: a pilot model of the human brain project approach J Am Med Inform Assoc 2001;8:34-48. - PMC - PubMed
    1. Nadkarni PM, Brandt C. Data extraction and ad hoc query of an entity-attribute-value database J Am Med Inform Assoc 1998;5:511-527. - PMC - PubMed
    1. Marenco L, Nadkarni P, Skoufos E, Shepherd G, Miller P. Neuronal database integration: the Senselab EAV data model Proc AMIA Symp 1999:102-106. - PMC - PubMed
    1. Chen RS, Nadkarni P, Marenco L, Levin F, Erdos J, Miller PL. Exploring performance issues for a clinical database organized using an entity-attribute-value representation J Am Med Inform Assoc 2000;7:475-487. - PMC - PubMed

Publication types