{"doi":"10.1073/pnas.2023202118","title":"A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases","abstract":"Despite remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This gap persists, even though many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases, and all of them encompass large amounts of viral sequence data. The lack of a comprehensive database for human-associated viruses has historically stymied efforts to interrogate the impact of the virome on human health. This study probes thousands of datasets to uncover sequences from over 45,000 unique virus taxa, with historically high per-genome completeness. Large publicly available case-control studies are reanalyzed, and over 2,200 strong virus-disease associations are found.","journal":"Proceedings of the National Academy of Sciences","year":2021,"id":145876,"datarank":4.581822918042325,"base_score":5.69035945432406,"endowment":5.69035945432406,"self_citation_contribution":0.8535539181486091,"citation_network_contribution":3.7282689998937157,"self_endowment_contribution":0.8535539181486091,"citer_contribution":3.7282689998937157,"corpus_percentile":95.22704417111473,"corpus_rank":618,"citation_count":295,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7188,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":75.0,"fair_percentile":95.6282482421278,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":434178,"name":"Christopher B. Buck","orcid":"0000-0003-3165-8094","position":1,"is_corresponding":false},{"id":619143,"name":"Michael J. Tisza","orcid":"0000-0003-1168-1617","position":0,"is_corresponding":true}],"reference_count":115,"raw_metadata":null,"created_at":"2026-07-18T23:42:12.871665Z","pmid":"34083435","pmcid":"PMC8201803","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":77.7778,"fair_a":68.75,"fair_i":100.0,"fair_r":58.3333,"fair_zscore":1.6051,"fair_rationale":{"fair_score":75.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":77.78,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All unique virus genomes with metadata and annotated genome maps have been deposited to GenBank under BioProject PRJNA573942.","grounded":false,"rationale":"The paper gives the BioProject accession PRJNA573942, a persistent identifier. [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":1.0,"verdict":"yes","evidence":"All unique virus genomes with metadata and annotated genome maps have been deposited to GenBank under BioProject PRJNA573942","grounded":true,"rationale":"GenBank is a named data repository. [majority verdict 'yes' (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":1.0,"verdict":"yes","evidence":"Data Availability Fasta sequence files from CHVD databases can be accessed at ( https://zenodo.org/record/4498884 ) ( 56 ). Additionally, all unique virus genomes with metadata and annotated genome maps have been deposited to GenBank under BioProject PRJNA573942 . Accession numbers for individual virus OTUs can be found in Dataset S2 .","grounded":true,"rationale":"The statement points to repository records with accessions and links. [majority verdict 'yes' (4/5 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 analysis resulted in over 180,000 putative viral sequences. The sequences were classified into operational taxonomic units (OTUs) by clustering at 95% average nucleotide identity across 85% of contig length, according to the community-recommended standard ( 54 , 55 ) ( Materials and Methods ). A final database of 45,033 sequences representing nonredundant virus OTUs was generated ( Fig. 1 ), and this database will herein be referred to as the Cenote Human Virome Database (CHVD, download available at https://zenodo.org/record/4498884 ) ( 56 ).","grounded":true,"rationale":"The paper describes the dataset's content in running prose, but no itemised inventory within the paper text. [majority verdict 'partial' (2/5 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":1.0,"verdict":"yes","evidence":"M. J. Tisza , Virus sequences and data tables related to the Cenote Human Virome Database v1.1. Zenodo. https://zenodo.org/record/4498884 . Deposited 2 February 2021.","grounded":true,"rationale":"The dataset appears as a reference-list entry (reference 56).","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":68.75,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Fasta sequence files from CHVD databases can be accessed at ( https://zenodo.org/record/4498884 ) ( 56 ).","grounded":true,"rationale":"The Zenodo link is given with no stated precondition. [majority verdict 'yes' (4/5 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":"Fasta sequence files from CHVD databases can be accessed at ( https://zenodo.org/record/4498884 ) ( 56 ).","grounded":true,"rationale":"The paper describes the action of accessing the data but does not label the access level. [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":null,"grounded":false,"rationale":"The data are not sensitive human data; no gatekeeper is mentioned.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"All submitted sequences/genomes are associated with Bioproject PRJNA573942 and will be released upon publication of this manuscript.","grounded":true,"rationale":"The paper states an availability timing (upon publication) but no persistence commitment.","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":100.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Fasta sequence files from CHVD databases can be accessed at ( https://zenodo.org/record/4498884 ) ( 56 ).","grounded":true,"rationale":"FASTA is an open file format.","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":1.0,"verdict":"yes","evidence":"according to the community-recommended standard ( 54 , 55 )","grounded":true,"rationale":"The paper references MIUViG (minimum information about an uncultivated virus genome) as a community standard applied to the data. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"Analysis of read data from PRJEB17784, a case-control study of stool samples from patients with or without Parkinson’s disease.","grounded":true,"rationale":"The paper gives an identifier (PRJEB17784) for an external resource.","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":58.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).","grounded":false,"rationale":"The paper does not state a license for the data; the CC license applies to the article only.","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":"Cenote-Taker 2 ( 33 ) was used to check contigs for two common end features of complete viral genomes","grounded":true,"rationale":"The paper names the specific software tool (Cenote-Taker 2) used to produce the data, which is a named tool. [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":0.5,"verdict":"partial","evidence":"Dataset S2 provides spreadsheet information on each virus, including OTU, hallmark genes, CRISPR hits (see Fig. 2 ), and statistical information.","grounded":true,"rationale":"Variable definitions are provided in a supplementary table inside the article.","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":"Best representative sequences from aniclust.py were used as virus OTU exemplars comprising the CHVD version 1.1.","grounded":true,"rationale":"The paper names a version token: 'CHVD version 1.1'.","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Cenote-Taker 2 ( https://github.com/mtisza1/Cenote-Taker2 , https://cyverse.org/discovery-environment )","grounded":true,"rationale":"The paper provides a GitHub URL for the study's own 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":"HHS | NIH | National Cancer Institute (NCI) 100000054 ZIA BC011090 Michael Tisza Christopher B Buck","grounded":true,"rationale":"The paper gives a grant number (ZIA BC011090).","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":"This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).","why":"The paper does not state a license for the data; the CC license applies to the article only.","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":"All unique virus genomes with metadata and annotated genome maps have been deposited to GenBank under BioProject PRJNA573942.","why":"The paper gives the BioProject accession PRJNA573942, a persistent identifier. [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_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 analysis resulted in over 180,000 putative viral sequences. The sequences were classified into operational taxonomic units (OTUs) by clustering at 95% average nucleotide identity across 85% of contig length, according to the community-recommended standard ( 54 , 55 ) ( Materials and Methods ). A final database of 45,033 sequences representing nonredundant virus OTUs was generated ( Fig. 1 ), and this database will herein be referred to as the Cenote Human Virome Database (CHVD, download available at https://zenodo.org/record/4498884 ) ( 56 ).","why":"The paper describes the dataset's content in running prose, but no itemised inventory within the paper text. [majority verdict 'partial' (2/5 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":"partial","current":0.5,"evidence":"Fasta sequence files from CHVD databases can be accessed at ( https://zenodo.org/record/4498884 ) ( 56 ).","why":"The paper describes the action of accessing the data but does not label the access level. [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":"Dataset S2 provides spreadsheet information on each virus, including OTU, hallmark genes, CRISPR hits (see Fig. 2 ), and statistical information.","why":"Variable definitions are provided in a supplementary table inside the article.","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are not sensitive human data; no gatekeeper is mentioned.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All submitted sequences/genomes are associated with Bioproject PRJNA573942 and will be released upon publication of this manuscript.","why":"The paper states an availability timing (upon publication) but no persistence commitment.","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).","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.","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.","Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:52:12.572626Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}