{"doi":"10.1038/s41597-019-0286-0","title":"Experiment design driven FAIRification of omics data matrices, an exemplar","abstract":"We outline a principled approach to data FAIRification rooted in the notions of experimental design, and whose main intent is to clarify the semantics of data matrices. Using two related metabolomics datasets associated to journal articles, we perform retrospective data and metadata curation and re-annotation, using community, open, interoperability standards. The results are semantically-anchored data matrices, deposited in public archives, which are readable by software agents for data-level queries, and which can support the reproducibility and reuse of the data underpinning the publications.","journal":"Scientific 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Philippe","orcid":"0000-0001-9853-5668","position":0,"is_corresponding":true}],"reference_count":23,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"31831744","pmcid":"PMC6908569","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":90.0,"fair_a":80.0,"fair_i":50.0,"fair_r":58.3333,"fair_zscore":2.2046,"fair_rationale":{"fair_score":69.58,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":90.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers 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states that all data and code are deposited in Zenodo with open licenses (CC-BY 4.0) and provides specific DOIs, ensuring open and unambiguous access."}]},"I":{"name":"Interoperable","score":50.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":1.0,"signal":null,"rationale":"The paper extensively uses community standards and formats (CHEBI, NCBI Taxonomy, Plant Ontology, STATO, InChI, Frictionless Tabular Data Package, JSON, RDF, SPARQL, ISA-Tab) to ensure interoperability."}]},"R":{"name":"Reusable","score":58.33,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":1.0,"signal":null,"rationale":"The paper provides a clear data-availability statement with DOIs, an open license (CC-BY 4.0) for data, and detailed reproducible workflows (Jupyter notebooks), strongly supporting reuse."}]}},"suggestions":["Explicitly state the license for the code repository (e.g., GitHub) to ensure full reusability.","Include machine-readable metadata for the paper itself using schema.org or similar to enhance findability.","Provide versioned citations for all ontologies used to improve provenance and reproducibility."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:47:50.224389Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}