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Ruben Verborgh

Interoperability and FAIRness through a novel combination of Web technologies

by Mark D. Wilkinson, Ruben Verborgh, Luiz Olavo Bonino da Silva Santos, Tim Clark, Morris Swertz, Fleur D. L. Kelpin, Alasdair J. G. Gray, Erik Schultes, Erik M. van Mulligen, Paolo Ciccarese, Arnold Kuzniar, Anand Gavai, Mark Thompson, Rajaram Kaliyaperumal, Jerven Bolleman, and Michel Dumontier

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved at the level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs.

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Published in 2017 in PeerJ Computer Science.


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Cite this article easily using its BibTeX entry:

  title = {Interoperability and {FAIRness} through a novel combination of {Web} technologies},
  author = {Wilkinson, Mark D. and Verborgh, Ruben and Bonino da Silva Santos, Luiz Olavo and Clark, Tim and Swertz, Morris and Kelpin, Fleur D. L. and Gray, Alasdair J. G. and Schultes, Erik and van Mulligen, Erik M. and Ciccarese, Paolo and Kuzniar, Arnold and Gavai, Anand and Thompson, Mark and Kaliyaperumal, Rajaram and Bolleman, Jerven and Dumontier, Michel},
  journal = {PeerJ Computer Science},
  year = 2017,
  month = apr,
  volume = 3,
  pages = {e110},
  issn = {2376-5992},
  url = {https://peerj.com/articles/cs-110/},
  doi = {10.7717/peerj-cs.110},

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M. D. Wilkinson, R. Verborgh, L. O. Bonino da Silva Santos, T. Clark, M. Swertz, F. D. L. Kelpin, A. J. G. Gray, E. Schultes, E. M. van Mulligen, P. Ciccarese, A. Kuzniar, A. Gavai, M. Thompson, R. Kaliyaperumal, J. Bolleman, and M. Dumontier, “Interoperability and FAIRness through a novel combination of Web technologies,” PeerJ Computer Science, vol. 3, p. e110, Apr. 2017.
Mark D. Wilkinson et al. 2017. Interoperability and FAIRness through a novel combination of Web technologies. PeerJ Computer Science 3 (April 2017), e110.
Wilkinson, M.D., Verborgh, R., Bonino da Silva Santos, L.O., Clark, T., Swertz, M., Kelpin, F.D.L., Gray, A.J.G., Schultes, E., van Mulligen, E.M., Ciccarese, P., Kuzniar, A., Gavai, A., Thompson, M., Kaliyaperumal, R., Bolleman, J., Dumontier, M.: Interoperability and FAIRness through a novel combination of Web technologies. PeerJ Computer Science. 3, e110 (2017).
Wilkinson, M. D., Verborgh, R., Bonino da Silva Santos, L. O., Clark, T., Swertz, M., Kelpin, F. D. L., … Dumontier, M. (2017). Interoperability and FAIRness through a novel combination of Web technologies. PeerJ Computer Science, 3, e110.
Wilkinson, Mark D. et al. “Interoperability and FAIRness through a Novel Combination of Web Technologies.” PeerJ Computer Science 3 (2017): e110. Print.

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