Comparison Between Graph Databases and RDF Engines for Modelling Epidemiological Investigation of Nosocomial Infections

Lorena Pujante-Otalora, Manuel Campos, Manuel Campos, Jose Juarez, Maria-Esther Vidal

2024

Abstract

We have evaluated the performance of property and knowledge graph databases in the context of spatiotemporal epidemiological investigation of an infection outbreak in a hospital. Specifically, we have chosen Neo4j as graph database, and GraphDB for knowledge graphs defined following RDF and its extension RDF*. We have defined a domain model describing a hospital layout and patient movements. For performance comparison, we have created ten graphs with different sizes based on MIMIC-III, implemented three epidemiological queries in Cypher, SPARQL and SPARQL* and defined three benchmarks that measure the execution time and main memory consumption of the three queries in each graph and database engine. Our research suggests that query complexity is a more determinant factor than graph size in the performance of the query executions. Neo4j presents better times and memory consumption than GraphDB for simple queries, but GraphDB is more efficient when traversing big subgraphs. Between RDF and RDF*, RDF* offers a more compact and human-friendly modelling and a better performance of the query execution.

Paper Citation

in Harvard Style

Pujante-Otalora L., Campos M., Juarez J. and Vidal M. (2024). Comparison Between Graph Databases and RDF Engines for Modelling Epidemiological Investigation of Nosocomial Infections. In Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 2: HEALTHINF; ISBN 978-989-758-688-0, SciTePress, pages 23-36. DOI: 10.5220/0012319900003657

in Bibtex Style

@conference{healthinf24,
author={Lorena Pujante-Otalora and Manuel Campos and Jose Juarez and Maria-Esther Vidal},
title={Comparison Between Graph Databases and RDF Engines for Modelling Epidemiological Investigation of Nosocomial Infections},
booktitle={Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 2: HEALTHINF},
year={2024},
pages={23-36},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0012319900003657},
isbn={978-989-758-688-0},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 2: HEALTHINF
TI - Comparison Between Graph Databases and RDF Engines for Modelling Epidemiological Investigation of Nosocomial Infections
SN - 978-989-758-688-0
AU - Pujante-Otalora L.
AU - Campos M.
AU - Juarez J.
AU - Vidal M.
PY - 2024
SP - 23
EP - 36
DO - 10.5220/0012319900003657
PB - SciTePress