{"doi":"10.1128/mra.01026-24","title":"Whole-genome sequences of six <i>Borrelia recurrentis</i> strains obtained via PacBio sequencing","abstract":"ABSTRACT Provided are whole-genome sequences of six Borrelia recurrentis strains that had been earlier isolated from louse-borne relapsing fever patients. The sequences of each genome presented here included one linear chromosome and 5 linear plasmids, whose average size was 1,284,895 bp with the mean GC content being 27.5%.","journal":"Microbiology Resource Announcements","year":2025,"id":560275,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":0.0,"corpus_rank":10477,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9508,"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":62.5,"fair_percentile":81.0149801284011,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1330219,"name":"John C. Blazier","orcid":"0000-0001-9712-0153","position":1,"is_corresponding":false},{"id":388377,"name":"Artem S. Rogovskyy","orcid":"0000-0001-6499-7928","position":2,"is_corresponding":false},{"id":1073142,"name":"Alhussien M. Gaber","orcid":"0000-0001-5303-3357","position":0,"is_corresponding":true}],"reference_count":19,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:55:42.883572Z","pmid":"39804060","pmcid":"PMC11895452","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":0.0,"fair_r":33.3333,"fair_zscore":1.1103,"fair_rationale":{"fair_score":62.5,"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":"The BioProject accession number is PRJNA1157803 .","grounded":true,"rationale":"The paper provides a BioProject accession, which is a persistent identifier in a recognized scheme. [majority verdict 'yes' (4/5 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":"The whole genome sequences of B. recurrentis strains A1, A11, A17, PAbJ, PBeK, and PAbN were deposited in the GenBank database under the following accession numbers: CP169982-CP169987 , CP169976-CP169981 , CP169970-CP169975 , CP169964-CP169969 , CP169958-CP169963 , and CP169952-CP169957 , respectively ( Table 1 ).","grounded":true,"rationale":"GenBank is a named repository in re3data. [majority verdict 'yes' (4/5 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":1.0,"verdict":"yes","evidence":"The whole genome sequences of B. recurrentis strains A1, A11, A17, PAbJ, PBeK, and PAbN were deposited in the GenBank database under the following accession numbers: CP169982-CP169987 , CP169976-CP169981 , CP169970-CP169975 , CP169964-CP169969 , CP169958-CP169963 , and CP169952-CP169957 , respectively ( Table 1 ).","grounded":true,"rationale":"The data availability statement points to a repository record with accessions. [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":"Each assembled B. recurrentis genome contained one chromosome and 5 linear plasmids ( Table 1 ).","grounded":true,"rationale":"The paper includes a table (Table 1) that itemizes the genome features and accession numbers, providing an itemised inventory.","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":"The whole genome sequences of B. recurrentis strains A1, A11, A17, PAbJ, PBeK, and PAbN were deposited in the GenBank database under the following accession numbers: CP169982-CP169987 , CP169976-CP169981 , CP169970-CP169975 , CP169964-CP169969 , CP169958-CP169963 , and CP169952-CP169957 , respectively ( Table 1 ).","grounded":true,"rationale":"The dataset identifiers appear only in the body text, not in the reference list. [majority verdict 'partial' (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":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":"The whole genome sequences of B. recurrentis strains A1, A11, A17, PAbJ, PBeK, and PAbN were deposited in the GenBank database under the following accession numbers: CP169982-CP169987 , CP169976-CP169981 , CP169970-CP169975 , CP169964-CP169969 , CP169958-CP169963 , and CP169952-CP169957 , respectively ( Table 1 ).","grounded":true,"rationale":"The paper states the data are deposited in public repositories without any precondition or embargo. [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":"The whole genome sequences of B. recurrentis strains A1, A11, A17, PAbJ, PBeK, and PAbN were deposited in the GenBank database under the following accession numbers: CP169982-CP169987 , CP169976-CP169981 , CP169970-CP169975 , CP169964-CP169969 , CP169958-CP169963 , and CP169952-CP169957 , respectively ( Table 1 ).","grounded":true,"rationale":"The paper describes the deposit actions but does not label the access level with a standard vocabulary term. [majority verdict 'partial' (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 whole genome sequences of B. recurrentis strains A1, A11, A17, PAbJ, PBeK, and PAbN were deposited in the GenBank database under the following accession numbers: CP169982-CP169987 , CP169976-CP169981 , CP169970-CP169975 , CP169964-CP169969 , CP169958-CP169963 , and CP169952-CP169957 , respectively ( Table 1 ).","grounded":true,"rationale":"The data are bacterial genomes and not identified as sensitive or human-subject data; no gatekeeper is named.","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":null,"grounded":false,"rationale":"The paper does not mention any retention period, persistence commitment, or availability timing beyond the act of deposit. [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":0.0,"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":"No file format is named 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":null,"grounded":false,"rationale":"No community standard vocabulary or checklist is named in the paper.","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":"Straains PAbJ (NR-51674), PBeK (NR-51672), and PAbN (NR-51673) were obtained through BEI Resources [National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), MD, USA].","grounded":false,"rationale":"The paper gives identifiers for the strains obtained from BEI Resources, which are external resources. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":null,"grounded":false,"rationale":"No license is named for the data; the article's CC BY license does not apply to the 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":"DNA samples were extracted using the Qiagen MagAtract HMW DNA kit (Qiagen, MI, USA) and sheared to an average size of 10–15 kb. Libraries prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences, CA, USA) were size-selected on the BluePippin instrument (Sage Science, MA, USA) to remove fragments of <10 kb, which excluded the smallest previously sequenced plasmid, lp6 ( 7 , 8 ). The library pool was sequenced with Sequel II Sequencing Kit 2.0 and 8M SMRT cell on the Sequel II instrument (Pacific Bioscience, CA, USA). De-novo assemblies were performed using IPA (SMRTtools version 11.0.0) at IGS. On the Grace computing cluster at Texas A&M University, PacBio reads were downsampled to 25K sequences per sample using seqtk (version 1.3) due to the extremely high coverage of the data set ( Table 1 ). The downsampled data were then assembled in Flye (version 2.9.1) under default parameters. Contigs were annotated using the NCBI Prokaryotic Genome Annotation Pipeline ( 15 ).","grounded":false,"rationale":"The paper names specific instruments, kits, and software with versions used to produce the data. [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":0.5,"verdict":"partial","evidence":"Each assembled B. recurrentis genome contained one chromosome and 5 linear plasmids ( Table 1 ).","grounded":true,"rationale":"Variable-level definitions are provided inside the article (Table 1), not as a separate documentation object.","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 version described in this paper is the first version.","grounded":true,"rationale":"The paper states a version token ('first version').","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":null,"grounded":false,"rationale":"No code availability is mentioned.","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":"This project was supported by three NIH NIAID awards: R03AI163601, R21AI182876, and T32OD011083.","grounded":true,"rationale":"The paper gives specific award numbers.","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 named for the data; the article's CC BY license does not apply to the 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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format is named 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":null,"why":"No code availability is mentioned.","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 clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The whole genome sequences of B. recurrentis strains A1, A11, A17, PAbJ, PBeK, and PAbN were deposited in the GenBank database under the following accession numbers: CP169982-CP169987 , CP169976-CP169981 , CP169970-CP169975 , CP169964-CP169969 , CP169958-CP169963 , and CP169952-CP169957 , respectively ( Table 1 ).","why":"The dataset identifiers appear only in the body text, not in the reference list. [majority verdict 'partial' (3/5 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":"The whole genome sequences of B. recurrentis strains A1, A11, A17, PAbJ, PBeK, and PAbN were deposited in the GenBank database under the following accession numbers: CP169982-CP169987 , CP169976-CP169981 , CP169970-CP169975 , CP169964-CP169969 , CP169958-CP169963 , and CP169952-CP169957 , respectively ( Table 1 ).","why":"The paper describes the deposit actions but does not label the access level with a standard vocabulary term. [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 clinical / human-subjects, describe the data with OMOP CDM, CDISC SDTM or HL7 FHIR.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No community standard vocabulary or checklist is named in the paper.","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":"DNA samples were extracted using the Qiagen MagAtract HMW DNA kit (Qiagen, MI, USA) and sheared to an average size of 10–15 kb. Libraries prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences, CA, USA) were size-selected on the BluePippin instrument (Sage Science, MA, USA) to remove fragments of <10 kb, which excluded the smallest previously sequenced plasmid, lp6 ( 7 , 8 ). The library pool was sequenced with Sequel II Sequencing Kit 2.0 and 8M SMRT cell on the Sequel II instrument (Pacific Bioscience, CA, USA). De-novo assemblies were performed using IPA (SMRTtools version 11.0.0) at IGS. On the Grace computing cluster at Texas A&M University, PacBio reads were downsampled to 25K sequences per sample using seqtk (version 1.3) due to the extremely high coverage of the data set ( Table 1 ). The downsampled data were then assembled in Flye (version 2.9.1) under default parameters. Contigs were annotated using the NCBI Prokaryotic Genome Annotation Pipeline ( 15 ).","why":"The paper names specific instruments, kits, and software with versions used to produce the data. [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":"partial","current":0.5,"evidence":"Each assembled B. recurrentis genome contained one chromosome and 5 linear plasmids ( Table 1 ).","why":"Variable-level definitions are provided inside the article (Table 1), not as a separate documentation object.","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 clinical / human-subjects data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The whole genome sequences of B. recurrentis strains A1, A11, A17, PAbJ, PBeK, and PAbN were deposited in the GenBank database under the following accession numbers: CP169982-CP169987 , CP169976-CP169981 , CP169970-CP169975 , CP169964-CP169969 , CP169958-CP169963 , and CP169952-CP169957 , respectively ( Table 1 ).","why":"The data are bacterial genomes and not identified as sensitive or human-subject data; no gatekeeper is 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":"Straains PAbJ (NR-51674), PBeK (NR-51672), and PAbN (NR-51673) were obtained through BEI Resources [National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), MD, USA].","why":"The paper gives identifiers for the strains obtained from BEI Resources, which are external resources. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","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 mention any retention period, persistence commitment, or availability timing beyond the act of deposit. [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.","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.","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).","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 clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) 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."],"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":"2026-07-20T13:57:54.113322Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}