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Editorial
. 2013 Dec 15;29(24):3107-8.
doi: 10.1093/bioinformatics/btt549. Epub 2013 Oct 17.

Are graph databases ready for bioinformatics?

Christian Theil Have  1 , Lars Juhl Jensen
Affiliations
Editorial

Are graph databases ready for bioinformatics?

Christian Theil Have et al. Bioinformatics. .

Abstract

Contact: Lars.Juhl.Jensen@gmail.com

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Figures

Fig. 1.
Fig. 1.
Relational versus graph database representation of a small protein interaction network. In the relational database, the network is stored as an interactions table (left). By contrast a graph database directly stores interactions as pointers between protein nodes (right). Below, we show the queries to identify second-order interaction partners in SQL and Cypher, respectively
See this image and copyright information in PMC

References

    1. Franceschini A, et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013;41:D808–D815. - PMC - PubMed
    1. Linding R, et al. Systematic discovery of in vivo phosphorylation networks. Cell. 2007;129:1415–1426. - PMC - PubMed
    1. Schriml LM, et al. Disease ontology: a backbone for disease semantic integration. Nucleic Acids Res. 2012;40:D940–D946. - PMC - PubMed
    1. Webber J, et al. Graph Databases. Sebastopol: O’Reilly Media; 2013.
    1. Zhou NF, et al. Proceedings of the 22nd International Conference on Tools with Artificial Intelligence (ICTAI) 2010. Mode-directed tabling for dynamic programming, machine learning and constraint solving; pp. 213–218.

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