{"doi":"10.1093/nar/gkaf1159","title":"Virus taxonomy: the database of the International Committee on Taxonomy of Viruses","abstract":"Taxonomic classification underlies all biological science and is the basis for comparative analysis of biological organisms and therefore our understanding of life. The International Committee on Taxonomy of Viruses (ICTV) develops the official taxonomy for all viruses. To ensure that the taxonomic data, associated metadata, and analytical tools used to search and visualize those data are easily accessible, the ICTV maintains a comprehensive database and website that provides these resources to the scientific community and the interested public. This report describes the extensive enhancements made to these resources since our first Nucleic Acids Research Database Issue publication in 2018. These enhancements have focused on improvements to the computational infrastructure supporting the database, website, and tools; expanding the information available on the taxonomy and the viruses classified by that taxonomy; enhancing existing and developing new tools to access, search, and display taxonomic data; expanding the available methods and links used to access the taxonomic and associated data; and providing outreach and training opportunities to our users to ensure that these resources are useful and used. The data and tools provided through this effort are available from the ICTV website at https://ictv.global.","journal":"Nucleic Acids Research","year":2025,"id":509730,"datarank":0.5638197276346703,"base_score":3.367295829986474,"endowment":3.367295829986474,"self_citation_contribution":0.5050943744979712,"citation_network_contribution":0.05872535313669903,"self_endowment_contribution":0.5050943744979712,"citer_contribution":0.05872535313669903,"corpus_percentile":65.26649648023516,"corpus_rank":4491,"citation_count":28,"citer_count":28,"citers_with_citation_signal":6,"citers_with_endowment":6,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9462,"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":81.25,"fair_percentile":98.68541730357688,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1364770,"name":"Caleb Powell","orcid":"0000-0002-0687-3481","position":1,"is_corresponding":false},{"id":838779,"name":"Donald M. Dempsey","orcid":"0000-0002-2200-5828","position":2,"is_corresponding":false},{"id":281180,"name":"R. Curtis Hendrickson","orcid":"0000-0001-6986-4630","position":3,"is_corresponding":false},{"id":1365624,"name":"Logan R Mims","orcid":null,"position":4,"is_corresponding":false},{"id":281181,"name":"Elliot J. Lefkowitz","orcid":"0000-0002-4748-4925","position":5,"is_corresponding":false},{"id":1365623,"name":"Eden J Black","orcid":null,"position":0,"is_corresponding":true}],"reference_count":33,"raw_metadata":null,"created_at":"2026-07-19T02:47:30.942539Z","pmid":"41296552","pmcid":"PMC12807731","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":60.0,"fair_r":70.8333,"fair_zscore":1.8524,"fair_rationale":{"fair_score":81.25,"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":1.0,"verdict":"yes","evidence":"Files containing the current taxonomic data, the MSL and VMR spreadsheets, and all publicly released source code have been assigned DOIs and are available from the ICTV Zenodo data repository","grounded":true,"rationale":"The paper explicitly states that the data have been assigned DOIs, a persistent identifier scheme. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Files containing the current taxonomic data, the MSL and VMR spreadsheets, and all publicly released source code have been assigned DOIs and are available from the ICTV Zenodo data repository","grounded":true,"rationale":"The paper names Zenodo as the repository holding the data, which is a recognised data repository.","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":"Files containing the current taxonomic data, the MSL and VMR spreadsheets, and all publicly released source code have been assigned DOIs and are available from the ICTV Zenodo data repository","grounded":true,"rationale":"The statement points to a repository record with DOIs, matching Colavizza category 3 (link to archived data in a public repository).","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":"Files containing the current taxonomic data, the MSL and VMR spreadsheets, and all publicly released source code have been assigned DOIs and are available from the ICTV Zenodo data repository","grounded":true,"rationale":"The dataset's content is described in running prose (a sentence) but without an itemised inventory such as a section, table, or list. 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[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":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":"Registration and logging in to the website are not required to access any of the available data or resources.","grounded":true,"rationale":"The paper gives a route to the data with no stated precondition; the data are stated to be accessible without registration or login.","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":"Registration and logging in to the website are not required to access any of the available data or resources.","grounded":true,"rationale":"The paper describes an action (no registration required) from which the access level (open access) can be inferred, but does not use an explicit access-level label like 'open access'. 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[majority verdict 'partial' (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":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"The application returns a summary of the BLAST hits along with an HTML file containing the sequence alignments and a CSV file containing the BLAST hit statistics.","grounded":true,"rationale":"The only format token ('CSV') is mentioned for a tool output, not for the released dataset; no format is named for the data itself. [majority verdict 'no' (4/5 passes agreed)]","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":"The International Committee on Taxonomy of Viruses (ICTV) develops the official taxonomy for all viruses.","grounded":true,"rationale":"The ICTV virus taxonomy is a community standard for virus classification, and the data themselves are that taxonomy. [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":"Entries include the virus name, isolate designation, suggested abbreviation, GenBank accession number(s), segment names, genome composition, and host or sample source.","grounded":true,"rationale":"The paper includes GenBank accession numbers as identifiers for external resources (genome sequences) that the data references. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":70.83,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Unless otherwise noted, all data, source code, and other information provided by the ICTV are provided under the Creative Commons Attribution 4.0 International license","grounded":true,"rationale":"The paper attaches an open standard licence (CC BY 4.0) 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not name specific instruments or software used to produce the taxonomic data; the process is described in generic terms. [majority verdict 'no' (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":"Entries include the virus name, isolate designation, suggested abbreviation, GenBank accession number(s), segment names, genome composition, and host or sample source.","grounded":true,"rationale":"The variable definitions are provided inside the article text rather than in a separate documentation object shipped with the data. 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[downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"The application code, database schema, and data dumps of all database tables that make the data programmatically accessible are available from public GitHub repositories ( https://github.com/ICTV-Virus-Knowledgebase ).","grounded":true,"rationale":"The paper gives a machine-resolvable locator (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":"Research reported in this publication was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Award Number U24AI162625.","grounded":true,"rationale":"The paper includes an award/grant number (U24AI162625) attached to 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":"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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"A second spreadsheet, the Virus Metadata Resource (VMR; https://ictv.global/vmr , https://doi.org/10.5281/zenodo.15042309 ; “Taxonomy” menu > “Virus Metadata Resource”), containing a list of virus exemplars for each virus species, is also available.","why":"The dataset's identifier (DOI) appears only in the body text, not as a reference-list entry. [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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The application returns a summary of the BLAST hits along with an HTML file containing the sequence alignments and a CSV file containing the BLAST hit statistics.","why":"The only format token ('CSV') is mentioned for a tool output, not for the released dataset; no format is named for the data itself. [majority verdict 'no' (4/5 passes agreed)]","gain":8.33,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"MSL40","why":"The paper includes version tokens such as 'MSL40' in Table 2, indicating a specific release. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","gain":2.08,"priority":"useful","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":"Files containing the current taxonomic data, the MSL and VMR spreadsheets, and all publicly released source code have been assigned DOIs and are available from the ICTV Zenodo data repository","why":"The dataset's content is described in running prose (a sentence) but without an itemised inventory such as a section, table, or list. [majority verdict 'partial' (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":"partial","current":0.5,"evidence":"Registration and logging in to the website are not required to access any of the available data or resources.","why":"The paper describes an action (no registration required) from which the access level (open access) can be inferred, but does not use an explicit access-level label like 'open access'. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not name specific instruments or software used to produce the taxonomic data; the process is described in generic terms. [majority verdict 'no' (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":"Entries include the virus name, isolate designation, suggested abbreviation, GenBank accession number(s), segment names, genome composition, and host or sample source.","why":"The variable definitions are provided inside the article text rather than in a separate documentation object shipped with the data. [majority verdict 'partial' (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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"Registration and logging in to the website are not required to access any of the available data or resources.","why":"The study's data are non-sensitive virus taxonomy data, and no gatekeeper is named because the data are openly accessible without any access control.","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":"Files containing the current taxonomic data, the MSL and VMR spreadsheets, and all publicly released source code have been assigned DOIs and are available from the ICTV Zenodo data repository","why":"The paper states that the data are currently available but does not specify a persistence commitment or a future availability timing. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["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.","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.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","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."],"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":"2026-07-20T11:40:08.123663Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}