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Ontological Representation of FAIR Principles: A Blueprint for FAIRer Data Sources

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Advanced Information Systems Engineering (CAiSE 2023)

Abstract

Guidelines to improve the Findability, Accessibility, Interoperability, and Reuse of datasets, known as FAIR principles, were introduced in 2016 to enable machines to perform automatic actions on a variety of digital objects, including datasets. Since then, the principles have been widely adopted by data creators and users worldwide with the ‘FAIR’ acronym becoming a common part of the vocabulary of data scientists. However, there is still some controversy on how datasets should be interpreted since not all datasets that are claimed to be FAIR, necessarily follow the principles. In this research, we propose the OntoUML FAIR Principles Schema, as an ontological representation of FAIR principles for data practitioners. The work is based on OntoUML, an ontologically well-founded language for Ontology-driven Conceptual Modeling. OntoUML is a proxy for ontological analysis that has proven effective in supporting the explanation of complex domains. Our schema aims to disentangle the intricacies of the FAIR principles’ definition, by resolving aspects that are ambiguous, under-specified, recursively-specified, or implicit. The schema can be considered as a blueprint, or a template to follow when the FAIR classification strategy of a dataset must be designed. To demonstrate the usefulness of the schema, we present a practical example based on genomic data and discuss how the results provided by the OntoUML FAIR Principles Schema contribute to existing data guidelines.

A. Bernasconi and A. García S.—should be regarded as Joint First Authors.

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References

  1. Ammar, A., et al.: A semi-automated workflow for FAIR maturity indicators in the life sciences. Nanomaterials 10(10), 2068 (2020)

    Article  Google Scholar 

  2. Bernasconi, A., et al.: META-BASE: a novel architecture for large-scale genomic metadata integration. IEEE/ACM Trans. Comput. Biol. Bioinf. 19(1), 543–557 (2022)

    Article  Google Scholar 

  3. Bernasconi, A., et al.: Semantic interoperability: ontological unpacking of a viral conceptual model. BMC Bioinform. 23(11), 491 (2022)

    Article  Google Scholar 

  4. Borst, P., et al.: Engineering ontologies. Int. J. Hum Comput. Stud. 46(2–3), 365–406 (1997)

    Article  Google Scholar 

  5. Buniello, A., et al.: The NHGRI-EBI GWAS catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47(D1), D1005–D1012 (2018)

    Article  Google Scholar 

  6. Devaraju, A., et al.: An automated solution for measuring the progress toward FAIR research data. Patterns 2(11), 100370 (2021)

    Article  Google Scholar 

  7. Garcia, L., et al.: FAIR adoption, assessment and challenges at UniProt. Sci. Data 6, 175 (2019)

    Article  Google Scholar 

  8. García S, A., et al.: An initial empirical assessment of an ontological model of the human genome. In: Guizzardi, R., Neumayr, B. (eds.) Advances in Conceptual Modeling. ER 2022. LNCS, vol. 13650, pp. 55–65. Springer, Cham (2022). https://doi.org/10.1007/978-3-031-22036-4_6

  9. García S. A. et al.: An ontological characterization of a conceptual model of the human genome. In: De Weerdt, J., Polyvyanyy, A. (eds.) Intelligent Information Systems. CAiSE 2022. LNBIP, vol. 452, pp. 27–35. Springer, Cham (2022). https://doi.org/10.1007/978-3-031-07481-3_4

  10. Griffo, C., Almeida, J.P.A., Guizzardi, G.: Conceptual modeling of legal relations. In: Trujillo, J.C., Davis, K.C., Du, X., Li, Z., Ling, T.W., Li, G., Lee, M.L. (eds.) ER 2018. LNCS, vol. 11157, pp. 169–183. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-00847-5_14

    Chapter  Google Scholar 

  11. Grossman, R.L., et al.: Toward a shared vision for cancer genomic data. N. Engl. J. Med. 375(12), 1109–1112 (2016)

    Article  Google Scholar 

  12. Guarino, N., Guizzardi, G.: We need to discuss the relationship: revisiting relationships as modeling constructs. In: Zdravkovic, J., Kirikova, M., Johannesson, P. (eds.) CAiSE 2015. LNCS, vol. 9097, pp. 279–294. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-19069-3_18

    Chapter  Google Scholar 

  13. Guerson, J., et al.: Onto UML lightweight editor: a model-based environment to build, evaluate and implement reference ontologies. In: IEEE EDOCW 2015 (2015)

    Google Scholar 

  14. Guizzardi, G.: Ontological foundations for structural conceptual models. CTIT, Centre for Telematics and Information Technology (2005)

    Google Scholar 

  15. Guizzardi, G.: Ontology, ontologies and the “I’’ of fair. Data Intell. 2, 181–191 (2020)

    Article  Google Scholar 

  16. Guizzardi, G., Bernasconi, A., Pastor, O., Storey, V.C.: Ontological unpacking as explanation: the case of the viral conceptual model. In: Ghose, A., Horkoff, J., Silva Souza, V.E., Parsons, J., Evermann, J. (eds.) ER 2021. LNCS, vol. 13011, pp. 356–366. Springer, Cham (2021). https://doi.org/10.1007/978-3-030-89022-3_28

    Chapter  Google Scholar 

  17. Guizzardi, G., et al.: UFO: unified foundational ontology. Appl. Ontol. 17(1), 167–210 (2022)

    Article  Google Scholar 

  18. Horrocks, I., et al.: From SHIQ and RDF to owl: the making of a web ontology language. J. Web Semant. 1(1), 7–26 (2003)

    Article  Google Scholar 

  19. Jacobsen, A., et al.: FAIR principles: interpretations and implementation considerations. Data Intell. 2(1–2), 10–29 (2020)

    Article  Google Scholar 

  20. Kersloot, M.G., et al.: Perceptions and behavior of clinical researchers and research support staff regarding data FAIRification. Sci. Data 9, 241 (2022)

    Article  Google Scholar 

  21. Kundaje, A., et al.: Integrative analysis of 111 reference human epigenomes. Nature 518(7539), 317–330 (2015)

    Article  Google Scholar 

  22. Mungall, C.J., et al.: Uberon, an integrative multi-species anatomy ontology. Genome Biol. 13, R5 (2012)

    Article  Google Scholar 

  23. Nayar, P.G., et al.: CardioGenBase: a literature based multi-omics database for major cardiovascular diseases. PLoS ONE 10(12), e0143188 (2015)

    Article  Google Scholar 

  24. O’Leary, N.A., et al.: Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucl. Acids Res. 44(D1), D733–D745 (2016)

    Article  Google Scholar 

  25. 1000 Genomes Project Consortium: A global reference for human genetic variation. Nature 526(7571), 68 (2015)

    Google Scholar 

  26. The UniProt Consortium: UniProt: the universal protein knowledgebase in 2021. Nucl. Acids Res. 49(D1), D480–D489 (2021)

    Article  Google Scholar 

  27. Ruy, F.B., et al.: From reference ontologies to ontology patterns and back. Data Knowl. Eng. 109, 41–69 (2017)

    Article  Google Scholar 

  28. Sansone, S.A., et al.: FAIRsharing as a community approach to standards, repositories and policies. Nat. Biotechnol. 37(4), 358–367 (2019)

    Article  Google Scholar 

  29. Schwanitz, V.J., et al.: Current state and call for action to accomplish findability, accessibility, interoperability, and reusability of low carbon energy data. Sci. Rep. 12, 5208 (2022)

    Article  Google Scholar 

  30. Bonino da Silva Santos, L.O., et al.: FAIR data point: a FAIR-oriented approach for metadata publication. Data Intell. (2022)

    Google Scholar 

  31. van der Velde, K.J., et al.: FAIR genomes metadata schema promoting next generation sequencing data reuse in Dutch healthcare and research. Sci. Data 9, 169 (2022)

    Article  Google Scholar 

  32. Verdonck, M., et al.: Comparing traditional conceptual modeling with ontology-driven conceptual modeling: an empirical study. Inf. Syst. 81, 92–103 (2019)

    Article  Google Scholar 

  33. Wilkinson, M.D., et al.: The FAIR guiding principles for scientific data management and stewardship. Sci. Data 3, 160018 (2016)

    Article  Google Scholar 

  34. Wilkinson, M.D., et al.: Evaluating FAIR maturity through a scalable, automated, community-governed framework. Sci. Data 6, 174 (2019)

    Article  Google Scholar 

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Acknowledgements

A.G.S. was supported by the Valencian Innovation Agency and Innovation through the OGMIOS project (INNEST/2021/57), the Generalitat Valenciana through the CoMoDiD project (CIPROM/2021/023), and the Spanish State Research Agency through the DELFOS (PDC2021-121243-I00,MICIN/AEI/10.13039/501 100011033) and SREC (PID2021-123824OB-I00) projects, and co-financed with ERDF and the European Union Next Generation EU/PRTR.

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Bernasconi, A., Simon, A.G., Guizzardi, G., Santos, L.O.B.d.S., Storey, V.C. (2023). Ontological Representation of FAIR Principles: A Blueprint for FAIRer Data Sources. In: Indulska, M., Reinhartz-Berger, I., Cetina, C., Pastor, O. (eds) Advanced Information Systems Engineering. CAiSE 2023. Lecture Notes in Computer Science, vol 13901. Springer, Cham. https://doi.org/10.1007/978-3-031-34560-9_16

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  • DOI: https://doi.org/10.1007/978-3-031-34560-9_16

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