ArticlePloS one2015
Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
14 citing papers in PubMed.
- Microbiome knowledge graph as a tool to understand bacteria-host associations.Archives of microbiology · 2025Article
- An epidemiological knowledge graph extracted from the World Health Organization's Disease Outbreak News.Scientific data · 2025Article
- An ontology-based knowledge graph for representing interactions involving RNA molecules.Scientific data · 2024Article
- Article
- Dealing with the Ambiguity of Glycan Substructure Search.Molecules (Basel, Switzerland) · 2021Article
- The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application.Glycobiology · 2021Article
- A consensus-based and readable extension ofBeilstein journal of organic chemistry · 2020Article
- glypy: An Open Source Glycoinformatics Library.Journal of proteome research · 2019Article
- A Bioinformatics View of Glycan⁻Virus Interactions.Viruses · 2019Review
- Glycomics@ExPASy: Bridging the Gap.Molecular & cellular proteomics : MCP · 2018Article
- Reducing vertices in property graphs.PloS one · 2018Article
- Article
- Knowledge Representation and Management: a Linked Data Perspective.Yearbook of medical informatics · 2016Review
- SugarBindDB, a resource of glycan-mediated host-pathogen interactions.Nucleic acids research · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Resource 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.
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