RESEARCH ARTICLE Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search Davide Alocci1,2, Julien Mariethoz1, Oliver Horlacher1,2, Jerven T. Bolleman3, Matthew P. Campbell4, Frederique Lisacek1,2* 1 Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland, 2 Computer Science Department, University of Geneva, Geneva, 1227, Switzerland, 3 Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland, 4 Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia *
[email protected] Abstract Resource description framework (RDF) and Property Graph databases are emerging tech- nologies that are used for storing graph-structured data. We compare these technologies OPEN ACCESS through a molecular biology use case: glycan substructure search. Glycans are branched Citation: Alocci D, Mariethoz J, Horlacher O, tree-like molecules composed of building blocks linked together by chemical bonds. The Bolleman JT, Campbell MP, Lisacek F (2015) molecular structure of a glycan can be encoded into a direct acyclic graph where each node Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search. PLoS ONE 10(12): represents a building block and each edge serves as a chemical linkage between two build- e0144578. doi:10.1371/journal.pone.0144578 ing blocks. In this context, Graph databases are possible software solutions for storing gly- Editor: Manuela Helmer-Citterich, University of can structures and Graph query languages, such as SPARQL and Cypher, can be used to Rome Tor Vergata, ITALY perform a substructure search. Glycan substructure searching is an important feature for Received: July 16, 2015 querying structure and experimental glycan databases and retrieving biologically meaning- ful data.