{"doi":"10.1128/mra.01273-24","title":"Draft genome of <i>Conoideocrella luteorostrata</i> ARSEF 14590 (Clavicipitaceae), an entomopathogenic fungus with a wealth of biosynthetic and biocontrol potential","abstract":"ABSTRACT The fungus Conoideocrella luteorostrata is a recently discovered pathogen of invasive elongate hemlock scale insects (EHS; Fiorinia externa ) in Christmas tree farms in the eastern U.S. Here, we report a scaffold-level genome and assembly along with an initial survey of biosynthetic gene clusters for strain ARSEF 14590 from EHS.","journal":"Microbiology Resource Announcements","year":2025,"id":570806,"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":10062,"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":0.8267,"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":33.3333,"fair_percentile":47.93641088352186,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":74767,"name":"Jason Stajich","orcid":"0000-0002-7591-0020","position":1,"is_corresponding":false},{"id":1295608,"name":"Hana Barrett","orcid":"0000-0002-5404-2922","position":2,"is_corresponding":false},{"id":19562,"name":"Lindsay R. Kasson","orcid":null,"position":3,"is_corresponding":false},{"id":463968,"name":"Daniel G. Panaccione","orcid":"0000-0002-4159-164X","position":4,"is_corresponding":false},{"id":1476722,"name":"Cecilia A. Reiter","orcid":null,"position":5,"is_corresponding":false},{"id":1476723,"name":"Jessica L. Fuss","orcid":null,"position":6,"is_corresponding":false},{"id":1476724,"name":"Gregory Biddle","orcid":null,"position":7,"is_corresponding":false},{"id":463967,"name":"Matthew T. Kasson","orcid":"0000-0001-5602-7278","position":8,"is_corresponding":false},{"id":920398,"name":"Brian Lovett","orcid":"0000-0002-5721-7695","position":0,"is_corresponding":true}],"reference_count":28,"raw_metadata":null,"created_at":"2026-07-19T02:57:11.713851Z","pmid":"40698771","pmcid":"PMC12352038","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":33.3333,"fair_a":25.0,"fair_i":0.0,"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":33.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JASWJB010000000 and the assembly under accession number GCA_032433595.1. Sequence reads were deposited under SRA project accession number SRX20698148, BioProject accession number PRJNA980380, and BioSample accession number SAMN35627742.","grounded":false,"rationale":"Multiple persistent identifiers in accepted schemes (GenBank, SRA, BioProject, etc.) are provided for the dataset. [downgraded to 'partial' — no verifiable quote from the paper]","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":"This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JASWJB010000000 and the assembly under accession number GCA_032433595.1.","grounded":false,"rationale":"The paper names DDBJ/ENA/GenBank as the repository holding the data, which is a recognized data repository. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":0.5,"verdict":"partial","evidence":"DATA AVAILABILITY This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JASWJB010000000 and the assembly under accession number GCA_032433595.1. Sequence reads were deposited under SRA project accession number SRX20698148, BioProject accession number PRJNA980380, and BioSample accession number SAMN35627742.","grounded":false,"rationale":"The data availability statement points to repository records with accessions, matching 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":0.0,"verdict":"no","evidence":"The assembled scaffold-level ( n = 864) genome for CL strain ARSEF 14590 was 47.39 Mbp (coverage, 51.6 x ; N 50 , 111.30 kb; L 50 , 126; G + C content, 49%).","grounded":false,"rationale":"The dataset's extent and content are described in running prose, but no itemised inventory (section, table, or list) specific to the data files is provided. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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":"This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JASWJB010000000 and the assembly under accession number GCA_032433595.1. Sequence reads were deposited under SRA project accession number SRX20698148, BioProject accession number PRJNA980380, and BioSample accession number SAMN35627742.","grounded":false,"rationale":"The dataset identifiers appear only in the body text (Data Availability section), not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":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":"This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JASWJB010000000 and the assembly under accession number GCA_032433595.1. Sequence reads were deposited under SRA project accession number SRX20698148, BioProject accession number PRJNA980380, and BioSample accession number SAMN35627742.","grounded":false,"rationale":"The data are deposited in public repositories without any stated precondition for access, implying unconditional availability. [downgraded to 'partial' — no verifiable quote from the paper]","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":"This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JASWJB010000000 and the assembly under accession number GCA_032433595.1. Sequence reads were deposited under SRA project accession number SRX20698148, BioProject accession number PRJNA980380, and BioSample accession number SAMN35627742.","grounded":false,"rationale":"The access level of the data is not explicitly labeled with terms like 'open access' or 'publicly available'; only a deposit statement is provided.","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 not sensitive; no gatekeeper is mentioned.","grounded":false,"rationale":"The dataset is a fungal genome, not human or sensitive data, and no access restrictions or gatekeeper are 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":"No sentence in the text states when the data become available or how long they persist; only the deposit is mentioned without any timeline.","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":"The paper does not explicitly name any file format for the deposited data; only generic terms like 'sequence reads' and 'assembly' are used.","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 such as a minimum information checklist or ontology is named for the data; only tools (antiSMASH, BUSCO) are mentioned.","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":"Default parameters were used or when specified, available in the pipeline code, parameters, and logfiles archived in Github and Zenodo (29).","grounded":false,"rationale":"The paper provides a DOI for the code pipeline (reference 29) and lists accessions for other genomes in Table 1, qualifying as identifiers for non-own 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 explicitly stated for the data; the CC-BY license on the article does not necessarily 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":1.0,"verdict":"yes","evidence":"An Illumina NextSeq 1000 (Marshall University Genomics Core Facility, Huntington, WV) generated 8.668M 2 × 150 bp paired sequence reads or 2.6 Gb from CL ARSEF 14590.","grounded":true,"rationale":"The paper names specific instruments, kits, and software versions used to produce the data (e.g., Illumina NextSeq 1000, Qiagen DNeasy PowerSoil Pro Kit, SPAdes v3.15.2). [majority verdict 'yes' (4/5 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, codebook, data dictionary) is mentioned as accompanying the data; the only description is in the article text. [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_032433595.1","grounded":true,"rationale":"The assembly accession includes a version suffix (.1), identifying the specific 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not provide a locator for code written specifically for this study; the only code reference is to a generic pipeline from another study. [majority verdict 'no' (2/5 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":"This project was funded by the Christmas Tree Promotion Board grants 20-10-WVU and 21-07-WVU.","grounded":true,"rationale":"The paper lists specific award/grant numbers attached to named funders (e.g., Christmas Tree Promotion Board grants 20-10-WVU and 21-07-WVU). [majority verdict 'yes' (4/5 passes agreed)]","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 explicitly stated for the data; the CC-BY license on the article does not necessarily apply to the data.","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":"This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JASWJB010000000 and the assembly under accession number GCA_032433595.1. Sequence reads were deposited under SRA project accession number SRX20698148, BioProject accession number PRJNA980380, and BioSample accession number SAMN35627742.","why":"Multiple persistent identifiers in accepted schemes (GenBank, SRA, BioProject, etc.) are provided for the dataset. [downgraded to 'partial' — no verifiable quote from the paper]","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":"This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JASWJB010000000 and the assembly under accession number GCA_032433595.1.","why":"The paper names DDBJ/ENA/GenBank as the repository holding the data, which is a recognized data repository. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 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":"This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JASWJB010000000 and the assembly under accession number GCA_032433595.1. Sequence reads were deposited under SRA project accession number SRX20698148, BioProject accession number PRJNA980380, and BioSample accession number SAMN35627742.","why":"The data are deposited in public repositories without any stated precondition for access, implying unconditional availability. [downgraded to 'partial' — no verifiable quote from the paper]","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":"This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JASWJB010000000 and the assembly under accession number GCA_032433595.1. Sequence reads were deposited under SRA project accession number SRX20698148, BioProject accession number PRJNA980380, and BioSample accession number SAMN35627742.","why":"The dataset identifiers appear only in the body text (Data Availability section), not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 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":null,"why":"The paper does not explicitly name any file format for the deposited data; only generic terms like 'sequence reads' and 'assembly' are used.","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":"The paper does not provide a locator for code written specifically for this study; the only code reference is to a generic pipeline from another study. [majority verdict 'no' (2/5 passes agreed)]","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 This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JASWJB010000000 and the assembly under accession number GCA_032433595.1. Sequence reads were deposited under SRA project accession number SRX20698148, BioProject accession number PRJNA980380, and BioSample accession number SAMN35627742.","why":"The data availability statement points to repository records with accessions, matching 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":"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":"no","current":0.0,"evidence":"The assembled scaffold-level ( n = 864) genome for CL strain ARSEF 14590 was 47.39 Mbp (coverage, 51.6 x ; N 50 , 111.30 kb; L 50 , 126; G + C content, 49%).","why":"The dataset's extent and content are described in running prose, but no itemised inventory (section, table, or list) specific to the data files is provided. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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":"This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JASWJB010000000 and the assembly under accession number GCA_032433595.1. Sequence reads were deposited under SRA project accession number SRX20698148, BioProject accession number PRJNA980380, and BioSample accession number SAMN35627742.","why":"The access level of the data is not explicitly labeled with terms like 'open access' or 'publicly available'; only a deposit statement is provided.","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 community standard such as a minimum information checklist or ontology is named for the data; only tools (antiSMASH, BUSCO) are mentioned.","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, codebook, data dictionary) is mentioned as accompanying the data; the only description is in the article text. [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":"The data are not sensitive; no gatekeeper is mentioned.","why":"The dataset is a fungal genome, not human or sensitive data, and no access restrictions or gatekeeper are 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":"Default parameters were used or when specified, available in the pipeline code, parameters, and logfiles archived in Github and Zenodo (29).","why":"The paper provides a DOI for the code pipeline (reference 29) and lists accessions for other genomes in Table 1, qualifying as identifiers for non-own 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":"No sentence in the text states when the data become available or how long they persist; only the deposit is mentioned without any timeline.","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":"2026-07-20T13:51:23.223247Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}