{"doi":"10.1128/mra.00111-23","title":"Complete Genome Sequence of Soil Bacterium <i>Burkholderia</i> sp. Strain FERM BP-3421, a Producer of Spliceostatins","abstract":"Here, we report the complete genome sequence of Burkholderia sp. strain FERM BP-3421, a bacterium isolated previously from a soil sample in Japan. Strain FERM BP-3421 produces spliceostatins, which are splicing modulatory antitumor agents that advanced to preclinical development. The genome is composed of four circular replicons of 3.90, 3.0, 0.59, and 0.24 Mbp.","journal":"Microbiology Resource Announcements","year":2023,"id":371015,"datarank":0.29188652235829704,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.0,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.0,"corpus_percentile":43.93130656764911,"corpus_rank":7202,"citation_count":6,"citer_count":1,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8525,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":33.3333,"fair_percentile":47.93641088352186,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":901797,"name":"Barbara I. Adaikpoh","orcid":"0000-0003-0894-9563","position":1,"is_corresponding":false},{"id":818253,"name":"Tuan Anh Tran","orcid":"0000-0002-7903-0004","position":2,"is_corresponding":false},{"id":433988,"name":"Alessandra S. Eustáquio","orcid":"0000-0002-7852-7844","position":3,"is_corresponding":false},{"id":1109503,"name":"Sylvia Kunakom","orcid":null,"position":0,"is_corresponding":true}],"reference_count":13,"raw_metadata":null,"created_at":"2026-07-19T01:15:45.330525Z","pmid":"37074205","pmcid":"PMC10190677","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":44.4444,"fair_a":25.0,"fair_i":20.0,"fair_r":33.3333,"fair_zscore":-0.0442,"fair_rationale":{"fair_score":33.33,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":44.44,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The raw sequence reads have been submitted to the SRA under accession numbers SRX18227412 (Nanopore) and SRX18227411 (Illumina), BioSample accession number SAMN31673526, and BioProject accession number PRJNA899914. The assembled genome sequence of Burkholderia sp. FERM BP-3421 has been deposited at GenBank under accession numbers CP117779, CP117780, CP117781, and CP117782, which are the versions described in this paper.","grounded":false,"rationale":"The paper provides persistent identifiers (SRA, BioSample, BioProject, GenBank accessions) for the dataset. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":0.5,"verdict":"partial","evidence":"The raw sequence reads have been submitted to the SRA under accession numbers SRX18227412 (Nanopore) and SRX18227411 (Illumina), BioSample accession number SAMN31673526, and BioProject accession number PRJNA899914. The assembled genome sequence of Burkholderia sp. FERM BP-3421 has been deposited at GenBank under accession numbers CP117779, CP117780, CP117781, and CP117782, which are the versions described in this paper.","grounded":false,"rationale":"The paper names SRA and GenBank, which are proper data repositories. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","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 availability. The raw sequence reads have been submitted to the SRA under accession numbers SRX18227412 (Nanopore) and SRX18227411 (Illumina), BioSample accession number SAMN31673526, and BioProject accession number PRJNA899914. The assembled genome sequence of Burkholderia sp. FERM BP-3421 has been deposited at GenBank under accession numbers CP117779, CP117780, CP117781, and CP117782, which are the versions described in this paper.","grounded":false,"rationale":"The data availability statement points to repositories with accession numbers, which is a category 3 link to archived data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":0.5,"verdict":"partial","evidence":"The genome is composed of four circular replicons of 3.90, 3.0, 0.59, and 0.24 Mbp.","grounded":true,"rationale":"The dataset's content is described in a running prose sentence, not in an itemised inventory. [majority verdict 'partial' (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":0.0,"verdict":"no","evidence":"The raw sequence reads have been submitted to the SRA under accession numbers SRX18227412 (Nanopore) and SRX18227411 (Illumina), BioSample accession number SAMN31673526, and BioProject accession number PRJNA899914. The assembled genome sequence of Burkholderia sp. FERM BP-3421 has been deposited at GenBank under accession numbers CP117779, CP117780, CP117781, and CP117782, which are the versions described in this paper.","grounded":false,"rationale":"The dataset identifiers appear only in the body text (data availability statement) and not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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":25.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The raw sequence reads have been submitted to the SRA under accession numbers SRX18227412 (Nanopore) and SRX18227411 (Illumina), BioSample accession number SAMN31673526, and BioProject accession number PRJNA899914. The assembled genome sequence of Burkholderia sp. FERM BP-3421 has been deposited at GenBank under accession numbers CP117779, CP117780, CP117781, and CP117782, which are the versions described in this paper.","grounded":false,"rationale":"The text gives a route to the data (SRA and GenBank) with no stated precondition such as embargo or registration. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":0.0,"verdict":"no","evidence":"The raw sequence reads have been submitted to the SRA under accession numbers SRX18227412 (Nanopore) and SRX18227411 (Illumina), BioSample accession number SAMN31673526, and BioProject accession number PRJNA899914. The assembled genome sequence of Burkholderia sp. FERM BP-3421 has been deposited at GenBank under accession numbers CP117779, CP117780, CP117781, and CP117782, which are the versions described in this paper.","grounded":false,"rationale":"The paper does not label the access level with a vocabulary term but describes the action of submission to repositories, from which open access can be inferred. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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":"The data are genome sequences of a soil bacterium, which are not sensitive or human-subject data.","grounded":false,"rationale":"The data are not sensitive or human-subject, so no gatekeeper is named, leading to a verdict of no.","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":0.0,"verdict":"no","evidence":"No sentence in the paper states when the data become available or how long they persist.","grounded":false,"rationale":"The paper does not mention any timing or persistence commitment for the data.","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":"No file format is explicitly named in the paper.","grounded":false,"rationale":"The paper does not mention any file format token for the released data.","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":"No community standard (e.g., MIAME, MIxS) is named in the paper.","grounded":false,"rationale":"The paper does not name any data or metadata community 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":1.0,"verdict":"yes","evidence":"accession no. KJ364655","grounded":true,"rationale":"The paper provides an accession number (KJ364655) for a 16S rRNA sequence from a prior study, which is a qualified reference to another resource. [majority verdict 'yes' (3/5 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":33.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"No reuse license is stated for the data.","grounded":false,"rationale":"The paper does not attach any licence to the data themselves.","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":1.0,"verdict":"yes","evidence":"Sequencing was performed using a FLO-MIN104 (v. R9) flow cell and a MinION instrument.","grounded":true,"rationale":"The paper names specific instruments and software versions used to produce the data.","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":"No documentation object (README, codebook) is mentioned as accompanying the data.","grounded":false,"rationale":"The paper does not mention any documentation object shipped with the data.","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":"which are the versions described in this paper.","grounded":true,"rationale":"The GenBank accession numbers serve as version tokens, and the text states they are the versions described. [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":0.0,"verdict":"no","evidence":"No code availability statement is present in the paper.","grounded":false,"rationale":"The paper does not provide any locator for custom code.","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":"under grant 1R01GM129344-01A1","grounded":true,"rationale":"The paper gives a specific grant number (1R01GM129344-01A1) from a named funder.","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":"No reuse license is stated for the data.","why":"The paper does not attach any licence to the data themselves.","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The raw sequence reads have been submitted to the SRA under accession numbers SRX18227412 (Nanopore) and SRX18227411 (Illumina), BioSample accession number SAMN31673526, and BioProject accession number PRJNA899914. The assembled genome sequence of Burkholderia sp. FERM BP-3421 has been deposited at GenBank under accession numbers CP117779, CP117780, CP117781, and CP117782, which are the versions described in this paper.","why":"The paper provides persistent identifiers (SRA, BioSample, BioProject, GenBank accessions) for the dataset. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The raw sequence reads have been submitted to the SRA under accession numbers SRX18227412 (Nanopore) and SRX18227411 (Illumina), BioSample accession number SAMN31673526, and BioProject accession number PRJNA899914. The assembled genome sequence of Burkholderia sp. FERM BP-3421 has been deposited at GenBank under accession numbers CP117779, CP117780, CP117781, and CP117782, which are the versions described in this paper.","why":"The paper names SRA and GenBank, which are proper data repositories. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The raw sequence reads have been submitted to the SRA under accession numbers SRX18227412 (Nanopore) and SRX18227411 (Illumina), BioSample accession number SAMN31673526, and BioProject accession number PRJNA899914. The assembled genome sequence of Burkholderia sp. FERM BP-3421 has been deposited at GenBank under accession numbers CP117779, CP117780, CP117781, and CP117782, which are the versions described in this paper.","why":"The text gives a route to the data (SRA and GenBank) with no stated precondition such as embargo or registration. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"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":"no","current":0.0,"evidence":"The raw sequence reads have been submitted to the SRA under accession numbers SRX18227412 (Nanopore) and SRX18227411 (Illumina), BioSample accession number SAMN31673526, and BioProject accession number PRJNA899914. The assembled genome sequence of Burkholderia sp. FERM BP-3421 has been deposited at GenBank under accession numbers CP117779, CP117780, CP117781, and CP117782, which are the versions described in this paper.","why":"The dataset identifiers appear only in the body text (data availability statement) and not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":8.33,"priority":"important","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":"No file format is explicitly named in the paper.","why":"The paper does not mention any file format token for the released data.","gain":8.33,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"No code availability statement is present in the paper.","why":"The paper does not provide any locator for custom code.","gain":8.33,"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 availability. The raw sequence reads have been submitted to the SRA under accession numbers SRX18227412 (Nanopore) and SRX18227411 (Illumina), BioSample accession number SAMN31673526, and BioProject accession number PRJNA899914. The assembled genome sequence of Burkholderia sp. FERM BP-3421 has been deposited at GenBank under accession numbers CP117779, CP117780, CP117781, and CP117782, which are the versions described in this paper.","why":"The data availability statement points to repositories with accession numbers, which is a category 3 link to archived data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The genome is composed of four circular replicons of 3.90, 3.0, 0.59, and 0.24 Mbp.","why":"The dataset's content is described in a running prose sentence, not in an itemised inventory. [majority verdict 'partial' (4/5 passes agreed)]","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":"no","current":0.0,"evidence":"The raw sequence reads have been submitted to the SRA under accession numbers SRX18227412 (Nanopore) and SRX18227411 (Illumina), BioSample accession number SAMN31673526, and BioProject accession number PRJNA899914. The assembled genome sequence of Burkholderia sp. FERM BP-3421 has been deposited at GenBank under accession numbers CP117779, CP117780, CP117781, and CP117782, which are the versions described in this paper.","why":"The paper does not label the access level with a vocabulary term but describes the action of submission to repositories, from which open access can be inferred. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":"No community standard (e.g., MIAME, MIxS) is named in the paper.","why":"The paper does not name any data or metadata community 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":"no","current":0.0,"evidence":"No documentation object (README, codebook) is mentioned as accompanying the data.","why":"The paper does not mention any documentation object shipped with the data.","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":"The data are genome sequences of a soil bacterium, which are not sensitive or human-subject data.","why":"The data are not sensitive or human-subject, so no gatekeeper is named, leading to a verdict of no.","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":"No sentence in the paper states when the data become available or how long they persist.","why":"The paper does not mention any timing or persistence commitment for the data.","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.","Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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."],"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":"2026-07-20T12:50:23.781983Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}