Dataset Publication Standards: Community Lessons from a Multi-Stakeholder Workshop on FAIR Implementation
References
- Abreu-Vicente, J. et al. (2026) ‘Integrating curation into scientific publishing to train AI models’, Bioinformatics, 42(1), p.
btaf685 . Available at: 10.1093/bioinformatics/btaf685 - Attafi, O.A. et al. (2024) ‘DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology’, GigaScience, 13, p.
giae094 . Available at: 10.1093/gigascience/giae094 - Boeckhout, M., Zielhuis, G.A. and Bredenoord, A.L. (2018) ‘The FAIR guiding principles for data stewardship: fair enough?’, European Journal of Human Genetics, 26(7), pp. 931–936. Available at: 10.1038/s41431-018-0160-0
- Cohen, T. et al. (2017) ‘A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge’, Database, 2017, p.
bax061 . Available at: 10.1093/database/bax061 - Edmunds, S.C. et al. (2026) ‘Integrating machine learning standards in disseminating machine learning research’, Data Science Journal, 25(1), p.
1 . Available at: 10.5334/dsj-2026-001 - Europe PMC. (no date) Annotations API. Available at:
https://europepmc.org/AnnotationsApi (Accessed: 31 July 2026). - Farrell, G. et al. (2026) ‘DOME Copilot: A resource to automate transparent reporting of artificial intelligence methods’, bioRxiv [Preprint]. Available at: 10.64898/2026.04.16.718888
- Ferguson, A.R. et al. (2014) ‘Big data from small data: data-sharing in the “long tail” of neuroscience’, Nature Neuroscience, 17(11), pp. 1442–1447. Available at: 10.1038/nn.3838
- Global Biodata Coalition. (2022)
Global core biodata resources: concept and selection process . Zenodo. Available at: 10.5281/zenodo.7468719 - Gobeill, J. et al. (2020) ‘SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts’, Nucleic Acids Research, 48(W1), pp. W12–W16. Available at: 10.1093/nar/gkaa328
- Gobeill, J. et al. (2025) ‘Unlocking the potential of PubMed Central supplementary data files’, Bioinformatics Advances, 5(1), p.
vbaf155 . Available at: 10.1093/bioadv/vbaf155 - Hatos, A. et al. (2021) ‘APICURON: a database to credit and acknowledge the work of biocurators’, Database, 2021, p.
baab019 . Available at: 10.1093/database/baab019 - Heidorn, P.B. (2008) ‘Shedding light on the dark data in the long tail of science’, Library Trends, 57(2), pp. 280–299. Available at: 10.1353/lib.0.0036
- Liechti, R. et al. (2017) ‘SourceData: a semantic platform for curating and searching figures’, Nature Methods, 14(11), pp. 1021–1022. Available at: 10.1038/nmeth.4471
- Pasche, E. et al. (2023) ‘From SIBiLS to Biodiversity PMC: foundations for the One Health Library’, Biodiversity Information Science and Standards, 7, p. 467. Available at: 10.3897/biss.7.111660
- Pattyn, F. et al. (2017) ‘Assessment of FAIRness of open data sources in life sciences’, Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Healthcare and Life Sciences (SWAT4 LS 2017). Rome, Italy,
4–7 December .CEUR Workshop Proceedings , vol. 2042. Available at: 10.6084/m9.figshare.6994094 - Pop, M. and Salzberg, S.L. (2015) ‘Use and mis-use of supplementary material in science publications’, BMC Bioinformatics, 16(1), p.
237 . Available at: 10.1186/s12859-015-0668-z - Rocca-Serra, P. et al. (2023) ‘The FAIR Cookbook – the essential resource for and by FAIR doers’, Scientific Data, 10(1), p.
292 . Available at: 10.1038/s41597-023-02166-3 - Rosonovski, S. et al. (2024) ‘Europe PMC in 2023’, Nucleic Acids Research, 52(D1), pp. D1668–D1676. Available at: 10.1093/nar/gkad1085
- Sarkans, U. et al. (2018) ‘The BioStudies database – one stop shop for all data supporting a life sciences study’, Nucleic Acids Research, 46(D1), pp. D1266–D1270. Available at: 10.1093/nar/gkx965
- Walsh, I. et al. (2021) ‘DOME: recommendations for supervised machine learning validation in biology’, Nature Methods, 18(10), pp. 1122–1127. Available at: 10.1038/s41592-021-01205-4
- Wilkinson, M.D. et al. (2016) ‘The FAIR guiding principles for scientific data management and stewardship’, Scientific Data, 3(1), pp. 1–9. Available at: 10.1038/sdata.2016.18
DOI: https://doi.org/10.5334/dsj-2026-038 | Journal eISSN: 1683-1470
Language: English
Page range: 38 - 38
Submitted on: Jul 31, 2026
Accepted on: Oct 5, 2026
Published on: Oct 19, 2026
Published by: Ubiquity Press
In partnership with: Paradigm Publishing Services
Keywords:
© 2026 Julien Gobeill, Matt Jeffryes, Melissa Harrison, Scott Edmunds, Thomas Lemberger, Mark Hahnel, Slava Tykhonov, Patrick Ruch, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.