FAIR in practice: minimum metadata schema for bioinformatics analytics by machines

Journal of Biomedical Semantics, vol. 17

Abstract

BACKGROUND: One pillar of FAIR principles adoption is Reusability by machines to enable for example more efficient data analytics in fields such as Bioinformatics. However, it is not clear to what extent current metadata exposed by datasets and tools in common repositories enable this. In practice, metadata often lacks in machine actionability due to incomplete standardised metadata and lack of ontological descriptions. RESULTS: In this work, we identified minimal metadata that is needed to improve the machine actionability of bioinformatics tools and proposed a schema to address current limitations. The schema consists of metadata properties for the identification, selection, validation, and execution of tools. We also aligned this metadata to the metadata of datasets, in order to improve their integration for analytics by machines. CONCLUSIONS: The identified minimal metadata improves the machine actionability of tools and data, and can be incorporated into platforms for tool and data sharing, and in FAIR infrastructures.

Authors 10

1. Daphne Wijnbergen corresponding Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center, Leiden, The Netherlands. d.wijnbergen@lumc.nl

   Leiden University Medical Center

2. Núria Queralt-Rosiñach Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center, Leiden, The Netherlands

   Leiden University Medical Center

3. Valérie Barbié

   SIB Swiss Institute of Bioinformatics

   Affiliation as printed

   Swiss Institute of Bioinformatics, Geneva, Switzerland

   Swiss Institute of Bioinformatics

4. Emma Verkinderen

   Université Libre de Bruxelles

   Affiliation as printed

   Université Libre de Bruxelles, Brussels, Belgium

   Université Libre de Bruxelles

5. Nirupama Benis

   Amsterdam UMC Location University of Amsterdam

   Affiliation as printed

   Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands

   Amsterdam UMC location University of Amsterdam

6. Annika Jacobsen Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center, Leiden, The Netherlands

   Leiden University Medical Center

7. Peter A.C. ’t Hoen

   Radboud University Medical Center

   Affiliation as printed

   Radboud University Medical Center, Nijmegen, The Netherlands

   Radboud University Medical Center

8. Claudio Carta

   Istituto Superiore di Sanità

   Affiliation as printed

   Istituto Superiore di Sanità, Rome, Italy

   Istituto Superiore di Sanità

9. Marco Roos Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center, Leiden, The Netherlands

   Leiden University Medical Center

10. Eleni Mina Aachen

    Leiden University Medical Center

    Affiliation as printed

    Leiden University Medical Center, Leiden, The Netherlands

    Leiden University Medical Center