Archives des mots-clés : Mark Thompson

Making FAIR Easy with FAIR Tools: From Creolization to Convergence

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Authors : Mark Thompson, Kees Burger, Rajaram Kaliyaperumal, Marco Roos, Luiz Olavo Bonino da Silva Santos

Since their publication in 2016 we have seen a rapid adoption of the FAIR principles in many scientific disciplines where the inherent value of research data and, therefore, the importance of good data management and data stewardship, is recognized.

This has led to many communities asking “What is FAIR?” and “How FAIR are we currently?”, questions which were addressed respectively by a publication revisiting the principles and the emergence of FAIR metrics.

However, early adopters of the FAIR principles have already run into the next question: “How can we become (more) FAIR?” This question is more difficult to answer, as the principles do not prescribe any specific standard or implementation.

Moreover, there does not yet exist a mature ecosystem of tools, platforms and standards to support human and machine agents to manage, produce, publish and consume FAIR data in a user-friendly and efficient (i.e., “easy”) way. In this paper we will show, however, that there are already many emerging examples of FAIR tools under development.

This paper puts forward the position that we are likely already in a creolization phase where FAIR tools and technologies are merging and combining, before converging in a subsequent phase to solutions that make FAIR feasible in daily practice.

DOI : https://doi.org/10.1162/dint_a_00031

Interoperability and FAIRness through a novel combination of Web technologies

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

URL : Interoperability and FAIRness through a novel combination of Web technologies

DOI : https://doi.org/10.7717/peerj-cs.110