Archives des mots-clés : Luiz Olavo Bonino da Silva Santos

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

Evaluating FAIR maturity through a scalable, automated, community-governed framework

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Authors : Mark D. Wilkinson, Michel Dumontier, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Mario Prieto, Dominique Batista, Peter McQuilton, Tobias Kuhn, Philippe Rocca-Serra, Mercѐ Crosas, Erik Schultes

Transparent evaluations of FAIRness are increasingly required by a wide range of stakeholders, from scientists to publishers, funding agencies and policy makers. We propose a scalable, automatable framework to evaluate digital resources that encompasses measurable indicators, open source tools, and participation guidelines, which come together to accommodate domain relevant community-defined FAIR assessments.

The components of the framework are: (1) Maturity Indicators – community-authored specifications that delimit a specific automatically-measurable FAIR behavior; (2) Compliance Tests – small Web apps that test digital resources against individual Maturity Indicators; and (3) the Evaluator, a Web application that registers, assembles, and applies community-relevant sets of Compliance Tests against a digital resource, and provides a detailed report about what a machine “sees” when it visits that resource.

We discuss the technical and social considerations of FAIR assessments, and how this translates to our community-driven infrastructure. We then illustrate how the output of the Evaluator tool can serve as a roadmap to assist data stewards to incrementally and realistically improve the FAIRness of their resources.

URL : Evaluating FAIR maturity through a scalable, automated, community-governed framework

DOI : https://doi.org/10.1038/s41597-019-0184-5

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