Comparison of Approaches for Querying Chemical Compounds

  • Vojtěch Šípek
  • Irena Holubová
  • Martin SvobodaEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11721)


Chemical compounds form a database with specific features that can be utilized for more efficient query processing. Currently, there exists no comparison of performance and memory usage of the respective and most efficient approaches on the same data set. In this paper, we address this lack of information and we create an unbiased benchmark of the most popular index building methods for subgraph querying of chemical databases. In addition, we compare the results with the performance of an SQL and a graph database for which there exist various unconfirmed hypotheses on their efficiency.


Chemical database Subgraph querying Graph database Subgraph isomorphism 


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Vojtěch Šípek
    • 1
  • Irena Holubová
    • 1
  • Martin Svoboda
    • 1
    Email author
  1. 1.Faculty of Mathematics and PhysicsCharles UniversityPragueCzech Republic

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