Property Graph vs RDF Triple Store : A Comparison on Glycan Substructure Search

Resource description framework (RDF) and Property Graph databases are emerging technologies that are used for storing graph-structured data. These technologies were compared for glycan substructure search. The molecular structure of a glycan can be encoded into a direct acyclic graph where each node represents a building block and each edge serves as a chemical linkage between two building blocks.

Graph databases are possible software solutions for storing glycan structures and Graph query languages can be used to perform a substructure search. In this study, 19,404 glycan structures were selected from GlycomeDB ( and modelled for being stored into a RDF triple store and a Property Graph. We then performed two different sets of searches and compared the query response times and the results from both technologies to assess performance and accuracy. Whereas the two implementations produced the same results, a difference in the query response times was noticed.