{"doi":"10.1093/molbev/msaf132","title":"Footprints of Worldwide Adaptation in Structured Populations of <i>Drosophila melanogaster</i> Through the Expanded DEST 2.0 Genomic Resource","abstract":"Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009 to 2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. For example, we showed that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatiotemporal patterns of genetic variation in this classic model system.","journal":"Molecular Biology and Evolution","year":2025,"id":512230,"datarank":0.3958585994422889,"base_score":2.639057329615259,"endowment":2.639057329615259,"self_citation_contribution":0.3958585994422889,"citation_network_contribution":0.0,"self_endowment_contribution":0.3958585994422889,"citer_contribution":0.0,"corpus_percentile":53.84079832907867,"corpus_rank":5965,"citation_count":13,"citer_count":7,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9478,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":79.1667,"fair_percentile":97.67655151329869,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":642257,"name":"Marta Coronado‐Zamora","orcid":"0000-0001-9779-9661","position":1,"is_corresponding":false},{"id":1371635,"name":"Mathieu Gautier","orcid":"0000-0001-7257-5880","position":2,"is_corresponding":false},{"id":642252,"name":"Martin Kapun","orcid":"0000-0002-3810-0504","position":3,"is_corresponding":false},{"id":1371636,"name":"Sonja Steindl","orcid":"0009-0007-5354-1950","position":4,"is_corresponding":false},{"id":642264,"name":"Lino Ometto","orcid":"0000-0002-2679-625X","position":5,"is_corresponding":false},{"id":1371637,"name":"Katja M. Hoedjes","orcid":"0000-0001-6090-232X","position":6,"is_corresponding":false},{"id":1371638,"name":"Julia Beets","orcid":"0009-0005-8375-9884","position":7,"is_corresponding":false},{"id":6837,"name":"R. Axel W. Wiberg","orcid":"0000-0002-8074-8670","position":8,"is_corresponding":false},{"id":1039175,"name":"Giovanni R Mazzeo","orcid":"0009-0008-0898-2041","position":9,"is_corresponding":false},{"id":1282311,"name":"David J. Bass","orcid":"0000-0001-7414-2747","position":10,"is_corresponding":false},{"id":1371639,"name":"Denys Radionov","orcid":"0000-0003-0138-1303","position":11,"is_corresponding":false},{"id":642293,"name":"Iryna Kozeretska","orcid":"0000-0002-6485-1408","position":12,"is_corresponding":false},{"id":1371640,"name":"Maria Zinchenko","orcid":"0000-0001-6485-3668","position":13,"is_corresponding":false},{"id":1371641,"name":"O. V. Protsenko","orcid":"0000-0002-6019-9731","position":14,"is_corresponding":false},{"id":642278,"name":"Svitlana Serga","orcid":"0000-0003-1875-3185","position":15,"is_corresponding":false},{"id":1371642,"name":"Cristina Amor‐Jimenez","orcid":"0009-0009-7822-8199","position":16,"is_corresponding":false},{"id":642260,"name":"Sònia Casillas","orcid":"0000-0001-8191-0062","position":17,"is_corresponding":false},{"id":95796,"name":"Alejandro Sánchez‐Gracia","orcid":"0000-0003-4543-4577","position":18,"is_corresponding":false},{"id":642283,"name":"Aleksandra Patenković","orcid":"0000-0001-5763-6294","position":19,"is_corresponding":false},{"id":642273,"name":"Amanda Glaser‐Schmitt","orcid":"0000-0002-1322-1000","position":20,"is_corresponding":false},{"id":642299,"name":"Antonio Barbadilla","orcid":"0000-0002-0374-1475","position":21,"is_corresponding":false},{"id":643533,"name":"Antonio J. Buendía-Ruíz","orcid":null,"position":22,"is_corresponding":false},{"id":1371643,"name":"Astra Clelia Bertelli","orcid":"0009-0002-3595-0498","position":23,"is_corresponding":false},{"id":1371644,"name":"Balázs Kiss","orcid":"0000-0003-2511-9094","position":24,"is_corresponding":false},{"id":642266,"name":"Banu Şebnem Önder","orcid":"0000-0002-3003-248X","position":25,"is_corresponding":false},{"id":1372348,"name":"Bélen Roldán Matrín","orcid":null,"position":26,"is_corresponding":false},{"id":1033435,"name":"Bregje Wertheim","orcid":"0000-0001-8555-1925","position":27,"is_corresponding":false},{"id":1371645,"name":"Candice Deschamps","orcid":"0000-0002-5167-5433","position":28,"is_corresponding":false},{"id":563694,"name":"Carlos Bustos","orcid":"0000-0002-1783-3063","position":29,"is_corresponding":false},{"id":1371646,"name":"Carlos Tinedo","orcid":"0009-0004-8038-9817","position":30,"is_corresponding":false},{"id":1372349,"name":"Christian Feller","orcid":null,"position":31,"is_corresponding":false},{"id":1371647,"name":"Christian Schlötterer","orcid":"0000-0003-4710-6526","position":32,"is_corresponding":false},{"id":1275820,"name":"Clancy Lawler","orcid":"0009-0007-1867-4969","position":33,"is_corresponding":false},{"id":1371648,"name":"Claudia Fricke","orcid":"0000-0002-0691-6779","position":34,"is_corresponding":false},{"id":642291,"name":"Cristina P. Vieira","orcid":"0000-0002-7139-2107","position":35,"is_corresponding":false},{"id":1166122,"name":"Cristina Vieira","orcid":"0000-0003-3414-3993","position":36,"is_corresponding":false},{"id":642289,"name":"Darren J. Obbard","orcid":"0000-0001-5392-8142","position":37,"is_corresponding":false},{"id":642261,"name":"Dorcas J. Orengo","orcid":"0000-0001-7911-3224","position":38,"is_corresponding":false},{"id":1371649,"name":"Doris Vela","orcid":"0000-0001-7690-7758","position":39,"is_corresponding":false},{"id":1371650,"name":"Eduardo Amat","orcid":"0000-0002-0962-777X","position":40,"is_corresponding":false},{"id":1371651,"name":"Élgion L. S. Loreto","orcid":"0000-0002-7586-8168","position":41,"is_corresponding":false},{"id":848219,"name":"Envel Kerdaffrec","orcid":"0000-0001-8667-6850","position":42,"is_corresponding":false},{"id":770038,"name":"Esra Durmaz Mitchell","orcid":"0000-0002-4345-2264","position":43,"is_corresponding":false},{"id":642262,"name":"Eva Puerma","orcid":"0000-0001-7261-187X","position":44,"is_corresponding":false},{"id":642275,"name":"Fabian Staubach","orcid":"0000-0002-8097-2349","position":45,"is_corresponding":false},{"id":1371652,"name":"M. Florencia Camus","orcid":"0000-0003-0626-6865","position":46,"is_corresponding":false},{"id":1371653,"name":"Hervé Colinet","orcid":"0000-0002-8806-3107","position":47,"is_corresponding":false},{"id":1371654,"name":"Jan Hrček","orcid":"0000-0003-0711-6447","position":48,"is_corresponding":false},{"id":1371655,"name":"Jesper Givskov Sørensen","orcid":"0000-0002-9149-3626","position":49,"is_corresponding":false},{"id":642267,"name":"Jessica K. 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Schou","orcid":"0000-0001-5521-5269","position":59,"is_corresponding":false},{"id":960384,"name":"Emmanuel D. Ladoukakis","orcid":"0000-0002-1123-5396","position":60,"is_corresponding":false},{"id":643534,"name":"Maria Josefa Gómez-Julián","orcid":null,"position":61,"is_corresponding":false},{"id":643535,"name":"Maria Luisa Espinosa-Jimenez","orcid":null,"position":62,"is_corresponding":false},{"id":642259,"name":"Maria Pilar García Guerreiro","orcid":"0000-0001-9951-1879","position":63,"is_corresponding":false},{"id":960383,"name":"Maria-Eleni Parakatselaki","orcid":"0000-0003-0150-6153","position":64,"is_corresponding":false},{"id":554120,"name":"Marija Savić Veselinović","orcid":"0000-0001-8461-4373","position":65,"is_corresponding":false},{"id":554121,"name":"Marija Tanasković","orcid":"0000-0003-1440-2257","position":66,"is_corresponding":false},{"id":554118,"name":"Marina Stamenković‐Radak","orcid":"0000-0002-6937-7282","position":67,"is_corresponding":false},{"id":642255,"name":"Margot Paris","orcid":"0000-0001-7328-3820","position":68,"is_corresponding":false},{"id":1371659,"name":"Marta Pascual","orcid":"0000-0002-6189-0612","position":69,"is_corresponding":false},{"id":1371660,"name":"Michael G. 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Nunez","orcid":"0000-0002-3171-8918","position":0,"is_corresponding":true}],"reference_count":172,"raw_metadata":null,"created_at":"2026-07-19T02:48:06.263458Z","pmid":"40824865","pmcid":"PMC12360290","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":94.4444,"fair_a":62.5,"fair_i":40.0,"fair_r":58.3333,"fair_zscore":1.77,"fair_rationale":{"fair_score":79.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":94.44,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Supplementary datasets can be found in Zenodo at https://doi.org/10.5281/zenodo.13731977 .","grounded":true,"rationale":"The paper provides a DOI for the supplementary datasets in Zenodo, which is a persistent identifier. 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[majority verdict 'yes' (3/5 passes agreed)]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Table 1 SNP calling information for DEST 2.0 across major autosomes and chromosome X","grounded":true,"rationale":"The paper includes Table 1, which is an itemised inventory of SNP calling information for the dataset.","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"All new sequences reported here for the first time are available on the SRA ( https://www.ncbi.nlm.nih.gov/sra ) at PRJNA993612 and PRJNA1263695.","grounded":true,"rationale":"The dataset identifiers (SRA accessions and Zenodo DOI) appear only in the body text, not in the reference list. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":62.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"All new sequences reported here for the first time are available on the SRA ( https://www.ncbi.nlm.nih.gov/sra ) at PRJNA993612 and PRJNA1263695.","grounded":true,"rationale":"The access route is given with no stated precondition: the data are directly available at the SRA. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"All data, tools, and supporting resources for the DEST 2.0 release... are freely available through the website ( https://dest.bio ).","grounded":false,"rationale":"The paper labels the data as 'freely available', which is a natural-language equivalent of open access. 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[majority verdict 'no' (3/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":40.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Bulk downloads of all compiled tracks are available in BigWig format ( Kent et al. 2010 ), and Pool-Seq files (in VCF format) can be accessed through a dedicated data directory.","grounded":true,"rationale":"The paper names BigWig and VCF as file formats, both of which are open and community-standard.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No named data or metadata community standard is explicitly applied to the data; FlyBase is a database, not a standard.","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No identifier for a non-own resource is provided in the text; only references to other works are given.","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":58.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No reuse license is stated for the data itself; the CC-BY-NC license applies only to the article. 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[majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"the current DEST release (version 2.0)","grounded":true,"rationale":"The paper explicitly states 'version 2.0' as a version token for the dataset. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Code is available in GitHub at: https://github.com/DEST-bio/DESTv2_data_paper and https://github.com/DEST-bio/DESTv2 .","grounded":true,"rationale":"The paper provides GitHub URLs for the code, which are machine-resolvable locators.","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"National Institutes of Health R35 GM119686","grounded":true,"rationale":"The paper lists multiple grant numbers, e.g., R35 GM119686 from NIH.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No reuse license is stated for the data itself; the CC-BY-NC license applies only to the article. [majority verdict 'no' (3/5 passes agreed)]","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All new sequences reported here for the first time are available on the SRA ( https://www.ncbi.nlm.nih.gov/sra ) at PRJNA993612 and PRJNA1263695.","why":"The dataset identifiers (SRA accessions and Zenodo DOI) appear only in the body text, not in the reference list. [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All data, tools, and supporting resources for the DEST 2.0 release... are freely available through the website ( https://dest.bio ).","why":"The paper labels the data as 'freely available', which is a natural-language equivalent of open access. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No named data or metadata community standard is explicitly applied to the data; FlyBase is a database, not a standard.","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Table 1 SNP calling information for DEST 2.0 across major autosomes and chromosome X","why":"Variable definitions are provided inside the article (Table 1), not as a separate documentation object shipped with the data. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are from Drosophila, not human subjects, so no gatekeeper is needed or named.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifier for a non-own resource is provided in the text; only references to other works are given.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not state any persistence commitment or retention period for the data. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T12:13:36.510927Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}