{"doi":"10.1093/jhered/esaf035","title":"A near chromosome-level assembly of the serpentine endemic columbine, <i>Aquilegia eximia</i>","abstract":"The flowering plant genus Aquilegia (columbine) is an important contributor to biodiversity and an example of both biotic and abiotic niche adaptation across much of the Northern Hemisphere, especially in California. Here we report a near-chromosome level draft genome assembly for A. eximia, a California endemic species. A. eximia is a serpentine-soil specialist and is very closely related to 2 columbine species also being studied for the California Conservation Genomics Project (CCGP), A. formosa (widespread) and A. pubescens (high alpine). Utilizing high throughput, long reads (PacBio) and chromatin capture (Omni-C), the A. eximia genome makes marked contiguity improvements compared to the existing reference genome for another North American columbine, A. coerulea \"Goldsmith.\" The A. eximia genome will also be more useful for aligning whole genome resequencing data from California columbines than the genomes for more distantly related columbine species, the Asian A. oxysepala var. kansuensis and the European A. vulgaris. Notably, we found evidence that A. eximia, A. coerulea \"Goldsmith,\" and A. vulgaris all share the same overall genome structure and differ from A. oxysepala var. kansuensis by the same reciprocal translocation. The A. eximia reference genome will be a valuable tool for identifying patterns of plant biodiversity across California for the CCGP, as well as for future population genomic and trait mapping studies.","journal":"Journal of Heredity","year":2025,"id":544718,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":22.178386323199504,"corpus_rank":9377,"citation_count":1,"citer_count":1,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9011,"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":70.8333,"fair_percentile":91.99021705900336,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":92291,"name":"Merly Escalona","orcid":"0000-0003-0213-4777","position":1,"is_corresponding":false},{"id":930029,"name":"Courtney Miller","orcid":"0000-0002-4347-6629","position":2,"is_corresponding":false},{"id":911241,"name":"Noravit Chumchim","orcid":"0000-0003-1139-9427","position":3,"is_corresponding":false},{"id":730421,"name":"Oanh Nguyen","orcid":"0000-0003-1492-2084","position":4,"is_corresponding":false},{"id":730420,"name":"Mohan P A Marimuthu","orcid":"0000-0001-6121-3286","position":5,"is_corresponding":false},{"id":24537,"name":"Samuel Sacco","orcid":"0000-0003-1227-8934","position":6,"is_corresponding":false},{"id":908281,"name":"Colin W Fairbairn","orcid":"0009-0007-8129-0095","position":7,"is_corresponding":false},{"id":911242,"name":"Eric Beraut","orcid":"0000-0002-4443-6282","position":8,"is_corresponding":false},{"id":730422,"name":"Erin Toffelmier","orcid":"0000-0001-6028-8497","position":9,"is_corresponding":false},{"id":730423,"name":"H. Bradley Shaffer","orcid":"0000-0002-5795-9242","position":10,"is_corresponding":false},{"id":315271,"name":"Scott A. Hodges","orcid":"0000-0002-0401-6072","position":11,"is_corresponding":false},{"id":1435633,"name":"J. W. C. Johns","orcid":null,"position":0,"is_corresponding":true}],"reference_count":45,"raw_metadata":null,"created_at":"2026-07-19T02:53:17.418915Z","pmid":"40492452","pmcid":"PMC12767194","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":83.3333,"fair_a":68.75,"fair_i":20.0,"fair_r":41.6667,"fair_zscore":1.4401,"fair_rationale":{"fair_score":70.83,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":83.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Data generated for this study are available under NCBI BioProject PRJNA808326.","grounded":true,"rationale":"The paper gives a repository accession (PRJNA808326, a BioProject ID) which is a persistent identifier scheme. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Data generated for this study are available under NCBI BioProject PRJNA808326.","grounded":true,"rationale":"The paper names NCBI (National Center for Biotechnology Information) as the repository, a curated archive listed in re3data.","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Data generated for this study are available under NCBI BioProject PRJNA808326. Raw sequencing data for sample AexPC6 (NCBI BioSample SAMN25872407) are deposited in the NCBI Short Read Archive (SRA) under SRR19156777 for PacBio HiFi sequencing data, and SRR19156775-6 for the Omni-C Illumina sequencing data. GenBank accessions for both primary and alternate assemblies are GCA_023053565.2 and GCA_023053535.2; and for genome sequences JALIGU000000000 and JALIGV000000000.","grounded":false,"rationale":"The data-availability statement points to NCBI repositories with specific accessions, fitting Colavizza category 3 (link to archived data in a public repository). [downgraded to 'partial' — no verifiable quote from the paper]","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 2. Metrics for the primary and alternate assemblies of the Aquilegia eximia genome.","grounded":true,"rationale":"The paper includes a table (Table 2) that itemises the assembly metrics, constituting an itemised inventory of the dataset. [majority verdict 'yes' (4/5 passes agreed)]","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":"Data generated for this study are available under NCBI BioProject PRJNA808326.","grounded":true,"rationale":"The dataset identifiers (BioProject, GenBank accessions, SRA) appear only in the body text (Data Availability section) and not as a reference-list entry, so the strongest location is body text.","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":68.75,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Data generated for this study are available under NCBI BioProject PRJNA808326.","grounded":true,"rationale":"The text states the data are available in a public repository (NCBI) with no stated precondition such as registration, embargo, or request.","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":"Data generated for this study are available under NCBI BioProject PRJNA808326.","grounded":true,"rationale":"The paper describes the action of accessing the data via NCBI BioProject but does not apply an explicit access-level label (e.g., 'open access'), meeting the definition of 'partial'. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are plant genome sequences, not sensitive human-subject data, so no gatekeeper is named or required.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"Data generated for this study are available under NCBI BioProject PRJNA808326.","grounded":true,"rationale":"The paper states the data are available now but does not commit to how long they will persist, qualifying as an availability-timing statement only. [majority verdict 'partial' (4/5 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":20.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not name any file format for the released data (e.g., FASTA, FASTQ), making it impossible to classify as open or proprietary.","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 data or metadata community standard (e.g., MIAME, MINSEQE, FASTA) is explicitly named; only software tools like BUSCO are mentioned, which are not registries standards. [majority verdict 'no' (3/5 passes agreed)]","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":1.0,"verdict":"yes","evidence":"A. vulgaris (NCBI accession GCA_964291885.1)","grounded":true,"rationale":"The paper gives an NCBI accession for the A. vulgaris genome, an external resource used for comparison. [majority verdict 'yes' (4/5 passes agreed)]","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":41.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No license is stated for the data; the article's CC BY 4.0 license applies to the paper itself, not the deposited data.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The HiFi SMRTbell library was sequenced ... on a PacBio Sequel IIe sequencer.","grounded":false,"rationale":"The paper names specific instruments and kits used to produce the data (PacBio Sequel IIe, Illumina NovaSeq 6000, etc.). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No documentation object (README, data dictionary, codebook) is named as accompanying the data; the paper's description of the assembly is part of the article itself. [majority verdict 'no' (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":"GCA_023053565.2","grounded":true,"rationale":"The GenBank accession GCA_023053565.2 includes a version suffix (.2), pinning the snapshot. [majority verdict 'yes' (3/5 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":"Assembly scripts and other data for the analyses presented can be found at the following GitHub repository: www.github.com/ccgproject/ccgp_assembly","grounded":true,"rationale":"The paper provides a GitHub repository URL for the study's own code, a machine-resolvable locator. [majority verdict 'yes' (3/5 passes agreed)]","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":"UC Award ID RSI-19-690224","grounded":true,"rationale":"The paper reports an award/grant number (RSI-19-690224) attached to a named funder (State of California via UC), meeting the requirement for a specific award identifier.","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 license is stated for the data; the article's CC BY 4.0 license applies to the paper itself, not the deposited data.","gain":16.67,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not name any file format for the released data (e.g., FASTA, FASTQ), making it impossible to classify as open or proprietary.","gain":8.33,"priority":"important","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":"Data generated for this study are available under NCBI BioProject PRJNA808326.","why":"The dataset identifiers (BioProject, GenBank accessions, SRA) appear only in the body text (Data Availability section) and not as a reference-list entry, so the strongest location is body text.","gain":4.17,"priority":"important","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Data generated for this study are available under NCBI BioProject PRJNA808326. Raw sequencing data for sample AexPC6 (NCBI BioSample SAMN25872407) are deposited in the NCBI Short Read Archive (SRA) under SRR19156777 for PacBio HiFi sequencing data, and SRR19156775-6 for the Omni-C Illumina sequencing data. GenBank accessions for both primary and alternate assemblies are GCA_023053565.2 and GCA_023053535.2; and for genome sequences JALIGU000000000 and JALIGV000000000.","why":"The data-availability statement points to NCBI repositories with specific accessions, fitting Colavizza category 3 (link to archived data in a public repository). [downgraded to 'partial' — no verifiable quote from the paper]","gain":0.0,"priority":"essential","scored":false},{"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":"Data generated for this study are available under NCBI BioProject PRJNA808326.","why":"The paper describes the action of accessing the data via NCBI BioProject but does not apply an explicit access-level label (e.g., 'open access'), meeting the definition of 'partial'. [majority verdict 'partial' (4/5 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 data or metadata community standard (e.g., MIAME, MINSEQE, FASTA) is explicitly named; only software tools like BUSCO are mentioned, which are not registries standards. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The HiFi SMRTbell library was sequenced ... on a PacBio Sequel IIe sequencer.","why":"The paper names specific instruments and kits used to produce the data (PacBio Sequel IIe, Illumina NovaSeq 6000, etc.). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","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":"no","current":0.0,"evidence":null,"why":"No documentation object (README, data dictionary, codebook) is named as accompanying the data; the paper's description of the assembly is part of the article itself. [majority verdict 'no' (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 plant genome sequences, not sensitive human-subject data, so no gatekeeper is named or required.","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":"partial","current":0.5,"evidence":"Data generated for this study are available under NCBI BioProject PRJNA808326.","why":"The paper states the data are available now but does not commit to how long they will persist, qualifying as an availability-timing statement only. [majority verdict 'partial' (4/5 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.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","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.","Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","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."],"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":"2026-07-20T13:40:21.983273Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}