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dc.contributor.authorAlocci, Davide
dc.contributor.authorMariethoz, Julien
dc.contributor.authorHorlacher, Oliver
dc.contributor.authorBolleman, Jerven
dc.contributor.authorCampbell, Matthew P.
dc.contributor.authorLisacek, Frederique
dc.date.accessioned2017-07-31T03:12:02Z
dc.date.available2017-07-31T03:12:02Z
dc.date.issued2015
dc.identifier.issn1932-6203
dc.identifier.doi10.1371/journal.pone.0144578
dc.identifier.urihttp://hdl.handle.net/10072/342829
dc.description.abstractResource description framework (RDF) and Property Graph databases are emerging technologies that are used for storing graph-structured data. We compare these technologies through a molecular biology use case: glycan substructure search. Glycans are branched tree-like molecules composed of building blocks linked together by chemical bonds. 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. In this context, Graph databases are possible software solutions for storing glycan structures and Graph query languages, such as SPARQL and Cypher, can be used to perform a substructure search. Glycan substructure searching is an important feature for querying structure and experimental glycan databases and retrieving biologically meaningful data. This applies for example to identifying a region of the glycan recognised by a glycan binding protein (GBP). In this study, 19,404 glycan structures were selected from GlycomeDB (www.glycome-db.org) 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. The two implementations produced the same results, but interestingly we noted a difference in the query response times. Qualitative measures such as portability were also used to define further criteria for choosing the technology adapted to solving glycan substructure search and other comparable issues.
dc.description.peerreviewedYes
dc.languageEnglish
dc.language.isoeng
dc.publisherPublic Library of Sciences
dc.relation.ispartofpagefrome0144578-1
dc.relation.ispartofpagetoe0144578-17
dc.relation.ispartofissue12
dc.relation.ispartofjournalPLoS One
dc.relation.ispartofvolume10
dc.subject.fieldofresearchBiochemistry and Cell Biology not elsewhere classified
dc.subject.fieldofresearchcode060199
dc.titleProperty Graph vs RDF triple store: A comparison on glycan substructure search
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
dcterms.licensehttp://creativecommons.org/licenses/by/4.0/
dc.description.versionVersion of Record (VoR)
gro.rights.copyright© 2015 Alocci et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
gro.hasfulltextFull Text
gro.griffith.authorCampbell, Matthew


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