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FAIRification of biomedical research data

2025· article· en· W4413001977 on OpenAlex

Why this work is in the frame

A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.

affAt least one author lists a Canadian institution in the pinned OpenAlex snapshot.

Bibliographic record

VenueJournal of Clinical Epidemiology · 2025
Typearticle
Languageen
FieldComputer Science
TopicResearch Data Management Practices
Canadian institutionsUniversity of Ottawa
FundersHORIZON EUROPE Marie Sklodowska-Curie ActionsEuropean Commission
KeywordsEpidemiologyKey (lock)Data scienceClinical epidemiologyMEDLINEMedicineComputer sciencePathologyBiologyComputer security

Abstract

fetched live from OpenAlex

The Findable, Accessible, Interoperable, and Reusable guiding principles promote Findability, Accessibility, Interoperability, and Reuse of data to enhance data management and stewardship. In biomedicine, particular ethical, legal, and technical barriers complicate research data sharing. To help researchers overcome these challenges, we propose a framework of FAIRification from three dimensions - scientific, technical, and legal/ethical. We advocate for prospective FAIRification of study data, starting with a strong emphasis on planning for data-sharing from the beginning. Reflective questions throughout the process guide researchers to reflect on their situation. Researchers should assess resources and feasibility, secure technical and legal support, consider stakeholder needs, and devise an appropriate data sharing process. Given the sensitivity of biomedical data, confidentiality and security require careful attention. The data sharing strategy should be finalized before the study starts and documented in relevant study materials. Technical preparation for data sharing follows planning. Data should be well-documented with a data dictionary and metadata to facilitate reuse and provided in an accessible format. The data can be hosted on a repository to promote sharing and reuse. While a secure repository provides the technical foundation for data protection, effective administration is required to enforce data use agreements and licensing. We also discuss the importance of subsequent management upon data upload. Continued support for researchers and data maintenance are essential for effective reuse. Examples and resources to facilitate FAIRification are included to help researchers navigate challenges and ensure biomedical data are FAIR and reusable.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.237
metaresearch head score (Gemma)0.473
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesMetaresearch, Open science
Consensus categoriesMetaresearch
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Methods · Consensus signal: Methods
Teacher disagreement score0.651
Threshold uncertainty score0.996

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.2370.473
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0010.000
Bibliometrics0.0010.001
Science and technology studies0.0000.001
Scholarly communication0.0000.006
Open science0.0100.003
Research integrity0.0000.001
Insufficient payload (model declined to judge)0.0000.000

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.871
GPT teacher head0.715
Teacher spread0.156 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it