{"doi":"10.1093/nar/gkad1003","title":"VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023","abstract":"The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with >3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes.","journal":"Nucleic Acids Research","year":2023,"id":315000,"datarank":3.5080538209788266,"base_score":5.556828061699537,"endowment":5.556828061699537,"self_citation_contribution":0.8335242092549308,"citation_network_contribution":2.6745296117238957,"self_endowment_contribution":0.8335242092549308,"citer_contribution":2.6745296117238957,"corpus_percentile":93.65668755318326,"corpus_rank":821,"citation_count":258,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9597,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":37.5,"fair_percentile":50.687863038826045,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":230476,"name":"B Kirtley Amos","orcid":"0000-0003-2152-2927","position":1,"is_corresponding":false},{"id":617077,"name":"Cristina Aurrecoechea","orcid":null,"position":2,"is_corresponding":false},{"id":1014773,"name":"Saikou Y. Bah","orcid":"0000-0002-0309-6509","position":3,"is_corresponding":false},{"id":615746,"name":"Matthieu Barba","orcid":"0000-0002-7882-8356","position":4,"is_corresponding":false},{"id":617078,"name":"Ana Barreto","orcid":null,"position":5,"is_corresponding":false},{"id":606710,"name":"Evelina Y. Basenko","orcid":"0000-0001-8611-5447","position":6,"is_corresponding":false},{"id":617079,"name":"Robert Belnap","orcid":null,"position":7,"is_corresponding":false},{"id":617080,"name":"Ann S. Blevins","orcid":null,"position":8,"is_corresponding":false},{"id":468301,"name":"Ulrike Böhme","orcid":"0000-0002-0248-5924","position":9,"is_corresponding":false},{"id":617081,"name":"John Brestelli","orcid":null,"position":10,"is_corresponding":false},{"id":779211,"name":"Stuart M. Brown","orcid":"0000-0002-0906-9907","position":11,"is_corresponding":false},{"id":615748,"name":"Danielle Callan","orcid":"0009-0009-3690-8372","position":12,"is_corresponding":false},{"id":615749,"name":"Lahcen Campbell","orcid":"0000-0002-6405-9162","position":13,"is_corresponding":false},{"id":615751,"name":"George K. Christophides","orcid":"0000-0002-3323-1687","position":14,"is_corresponding":false},{"id":615752,"name":"Kathryn Crouch","orcid":"0000-0001-9310-4762","position":15,"is_corresponding":false},{"id":1014774,"name":"Helen Davison","orcid":"0000-0002-4302-5756","position":16,"is_corresponding":false},{"id":52184,"name":"Jeremy D. DeBarry","orcid":"0000-0001-5718-2675","position":17,"is_corresponding":false},{"id":1015629,"name":"Richard Demko","orcid":null,"position":18,"is_corresponding":false},{"id":617083,"name":"Ryan Doherty","orcid":null,"position":19,"is_corresponding":false},{"id":617084,"name":"Yikun Duan","orcid":null,"position":20,"is_corresponding":false},{"id":1015630,"name":"Walter Dundore","orcid":null,"position":21,"is_corresponding":false},{"id":616188,"name":"Sarah Dyer","orcid":"0000-0001-5690-9633","position":22,"is_corresponding":false},{"id":617085,"name":"Dave Falke","orcid":null,"position":23,"is_corresponding":false},{"id":1015631,"name":"Steve Fischer","orcid":null,"position":24,"is_corresponding":false},{"id":617087,"name":"Bindu Gajria","orcid":null,"position":25,"is_corresponding":false},{"id":1015632,"name":"Daniel Galdi","orcid":null,"position":26,"is_corresponding":false},{"id":615754,"name":"Gloria I. Giraldo-Calderón","orcid":"0000-0003-0598-0143","position":27,"is_corresponding":false},{"id":479614,"name":"Omar S. Harb","orcid":"0000-0003-4446-6200","position":28,"is_corresponding":false},{"id":615755,"name":"Elizabeth I. Harper","orcid":"0000-0002-3547-1692","position":29,"is_corresponding":false},{"id":479615,"name":"Danica Helb","orcid":"0000-0001-9595-7769","position":30,"is_corresponding":false},{"id":617088,"name":"Connor Howington","orcid":null,"position":31,"is_corresponding":false},{"id":617089,"name":"Sufen Hu","orcid":null,"position":32,"is_corresponding":false},{"id":617090,"name":"Jay C. Humphrey","orcid":null,"position":33,"is_corresponding":false},{"id":617091,"name":"John Iodice","orcid":null,"position":34,"is_corresponding":false},{"id":74630,"name":"Andrew R. Jones","orcid":"0000-0001-6118-9327","position":35,"is_corresponding":false},{"id":480255,"name":"J. Judkins","orcid":null,"position":36,"is_corresponding":false},{"id":615757,"name":"Sarah Kelly","orcid":"0000-0002-0948-5927","position":37,"is_corresponding":false},{"id":52191,"name":"Jessica C. Kissinger","orcid":"0000-0002-6413-1101","position":38,"is_corresponding":false},{"id":343475,"name":"Nupur Kittur","orcid":null,"position":39,"is_corresponding":false},{"id":615758,"name":"Dae Kun Kwon","orcid":"0000-0002-5890-0306","position":40,"is_corresponding":false},{"id":617092,"name":"Kristopher Lamoureux","orcid":null,"position":41,"is_corresponding":false},{"id":263249,"name":"Wei Li","orcid":"0000-0001-9931-5990","position":42,"is_corresponding":false},{"id":615760,"name":"Disha Lodha","orcid":"0000-0002-1592-9395","position":43,"is_corresponding":false},{"id":615761,"name":"Robert M. MacCallum","orcid":"0000-0001-5070-4493","position":44,"is_corresponding":false},{"id":289565,"name":"G. Maslen","orcid":"0000-0001-7318-3678","position":45,"is_corresponding":false},{"id":516445,"name":"Mary Ann McDowell","orcid":"0000-0003-4115-8464","position":46,"is_corresponding":false},{"id":1014775,"name":"Jeremy S. Myers","orcid":"0009-0001-6228-6900","position":47,"is_corresponding":false},{"id":746091,"name":"Mustafa V. Nural","orcid":"0000-0002-1871-076X","position":48,"is_corresponding":false},{"id":299002,"name":"David S. Roos","orcid":"0000-0001-6725-4089","position":49,"is_corresponding":false},{"id":595959,"name":"Samuel S. C. Rund","orcid":"0000-0002-1701-7787","position":50,"is_corresponding":false},{"id":615762,"name":"Achchuthan Shanmugasundram","orcid":"0000-0003-2349-6929","position":51,"is_corresponding":false},{"id":615763,"name":"Vasily Sitnik","orcid":"0000-0002-4647-1874","position":52,"is_corresponding":false},{"id":617096,"name":"Drew Spruill","orcid":null,"position":53,"is_corresponding":false},{"id":615764,"name":"David Starns","orcid":"0000-0001-6583-9067","position":54,"is_corresponding":false},{"id":299003,"name":"Sheena Shah Tomko","orcid":"0000-0002-2355-2794","position":55,"is_corresponding":false},{"id":378676,"name":"Haiming Wang","orcid":"0000-0002-6156-258X","position":56,"is_corresponding":false},{"id":615765,"name":"Susanne Warrenfeltz","orcid":"0000-0002-9789-8878","position":57,"is_corresponding":false},{"id":617097,"name":"Robert Wieck","orcid":null,"position":58,"is_corresponding":false},{"id":615766,"name":"Paul A. Wilkinson","orcid":"0000-0002-8836-5439","position":59,"is_corresponding":false},{"id":479616,"name":"Jie Zheng","orcid":"0000-0002-2999-0103","position":60,"is_corresponding":false},{"id":105325,"name":"Jorge Álvarez-Jarreta","orcid":"0000-0002-0946-0957","position":0,"is_corresponding":true}],"reference_count":24,"raw_metadata":null,"created_at":"2026-07-19T01:06:02.898877Z","pmid":"37953350","pmcid":"PMC10767879","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":22.2222,"fair_a":25.0,"fair_i":60.0,"fair_r":33.3333,"fair_zscore":0.1208,"fair_rationale":{"fair_score":37.5,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":22.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org ), CryptoDB (https://cryptodb.org ), FungiDB (https://fungidb.org ), GiardiaDB (https://giardiadb.org ), MicrosporidiaDB (https://microsporidiadb.org ), PiroplasmaDB (https://piroplasmadb.org ), PlasmoDB (https://plasmodb.org ), ToxoDB (https://toxodb.org ), TrichDB (https://trichdb.org ), TriTrypDB (https://tritrypdb.org ), VectorBase (https://vectorbase.org ), and VEuPathDB (https://veupathdb.org ).","grounded":false,"rationale":"The paper provides URL addresses to the project websites but no persistent identifier (DOI, Handle, ARK, or repository accession) for the dataset. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":0.5,"verdict":"partial","evidence":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org ), CryptoDB (https://cryptodb.org ), FungiDB (https://fungidb.org ), GiardiaDB (https://giardiadb.org ), MicrosporidiaDB (https://microsporidiadb.org ), PiroplasmaDB (https://piroplasmadb.org ), PlasmoDB (https://plasmodb.org ), ToxoDB (https://toxodb.org ), TrichDB (https://trichdb.org ), TriTrypDB (https://tritrypdb.org ), VectorBase (https://vectorbase.org ), and VEuPathDB (https://veupathdb.org ).","grounded":false,"rationale":"The paper names VEuPathDB and its component projects as the holders of the data; VEuPathDB is a recognized bioinformatics resource center listed in re3data and FAIRsharing. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org), CryptoDB (https://cryptodb.org), FungiDB (https://fungidb.org), GiardiaDB (https://giardiadb.org), MicrosporidiaDB (https://microsporidiadb.org), PiroplasmaDB (https://piroplasmadb.org), PlasmoDB (https://plasmodb.org), ToxoDB (https://toxodb.org), TrichDB (https://trichdb.org), TriTrypDB (https://tritrypdb.org), VectorBase (https://vectorbase.org), and VEuPathDB (https://veupathdb.org).","grounded":false,"rationale":"The statement points to the repository websites (general download tools) rather than a specific repository record with an accession or DOI. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":"Table 1. VEuPathDB resources and organisms supported ... Number of datasets (release 65) ... 3036","grounded":false,"rationale":"The paper includes Table 1, which itemizes the VEuPathDB projects and the number of datasets, providing an inventory of the data. [downgraded to 'partial' — no verifiable quote from the paper] [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":0.0,"verdict":"no","evidence":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org ), CryptoDB (https://cryptodb.org ), FungiDB (https://fungidb.org ), GiardiaDB (https://giardiadb.org ), MicrosporidiaDB (https://microsporidiadb.org ), PiroplasmaDB (https://piroplasmadb.org ), PlasmoDB (https://plasmodb.org ), ToxoDB (https://toxodb.org ), TrichDB (https://trichdb.org ), TriTrypDB (https://tritrypdb.org ), VectorBase (https://vectorbase.org ), and VEuPathDB (https://veupathdb.org ).","grounded":false,"rationale":"The dataset's identifier (URL) appears only in the body text of the data-availability statement, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper]","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":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org ), CryptoDB (https://cryptodb.org ), FungiDB (https://fungidb.org ), GiardiaDB (https://giardiadb.org ), MicrosporidiaDB (https://microsporidiadb.org ), PiroplasmaDB (https://piroplasmadb.org ), PlasmoDB (https://plasmodb.org ), ToxoDB (https://toxodb.org ), TrichDB (https://trichdb.org ), TriTrypDB (https://tritrypdb.org ), VectorBase (https://vectorbase.org ), and VEuPathDB (https://veupathdb.org ).","grounded":false,"rationale":"The paper provides a direct route to the data via the VEuPathDB project websites with no stated precondition such as registration, embargo, or application. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org ), CryptoDB (https://cryptodb.org ), FungiDB (https://fungidb.org ), GiardiaDB (https://giardiadb.org ), MicrosporidiaDB (https://microsporidiadb.org ), PiroplasmaDB (https://piroplasmadb.org ), PlasmoDB (https://plasmodb.org ), ToxoDB (https://toxodb.org ), TrichDB (https://trichdb.org ), TriTrypDB (https://tritrypdb.org ), VectorBase (https://vectorbase.org ), and VEuPathDB (https://veupathdb.org ).","grounded":false,"rationale":"The paper states that all data are available from the download tools on the VEuPathDB project websites, describing an access action without using an explicit access-level label like 'open access' or 'freely available'. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not discuss sensitive data or any gatekeeper for access; the data are from public domain sources and no access restrictions are 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":0.0,"verdict":"no","evidence":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org ), CryptoDB (https://cryptodb.org ), FungiDB (https://fungidb.org ), GiardiaDB (https://giardiadb.org ), MicrosporidiaDB (https://microsporidiadb.org ), PiroplasmaDB (https://piroplasmadb.org ), PlasmoDB (https://plasmodb.org ), ToxoDB (https://toxodb.org ), TrichDB (https://trichdb.org ), TriTrypDB (https://tritrypdb.org ), VectorBase (https://vectorbase.org ), and VEuPathDB (https://veupathdb.org ).","grounded":false,"rationale":"The paper states that data are available now but does not specify how long they will persist, thus only an availability-timing statement is given. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 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":1.0,"verdict":"yes","evidence":"genome.fasta or GFF files","grounded":true,"rationale":"The paper names FASTA and GFF as downloadable file formats, both of which are open, community-standard formats.","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":0.5,"verdict":"partial","evidence":"Gene Ontology (GO) (3,4)","grounded":false,"rationale":"The paper mentions the Gene Ontology, a community-standard ontology, as used for functional annotation of the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":0.0,"verdict":"no","evidence":"Sequence Read Archive (1) (https://www.ncbi.nlm.nih.gov/sra)","grounded":false,"rationale":"The paper provides a URL and reference for the Sequence Read Archive, an external resource used by the study. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":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":"The paper does not state any license or reuse terms for the data; the Creative Commons license applies only to the article itself.","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":"OrthoMCL","grounded":false,"rationale":"The paper names a specific software tool (OrthoMCL) used in the data analysis pipeline. [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":0.0,"verdict":"no","evidence":"All data are available from the download tools on VEuPathDB project websites","grounded":true,"rationale":"The paper does not mention a README, data dictionary, or codebook accompanying the data, nor does it include a table inside the article defining variables. [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":"Release 65 (September 12, 2023) of VEuPathDB contains over 3000 data sets.","grounded":true,"rationale":"The paper specifies a version token ('Release 65') and a date for the data snapshot. [majority verdict 'yes' (4/5 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":0.5,"verdict":"partial","evidence":"Project code can be found at our GitHub repository (https://github.com/VEuPathDB).","grounded":false,"rationale":"The paper provides a URL to the project's GitHub repository for the code, which is a machine-resolvable locator. [downgraded to 'partial' — no verifiable quote from the paper]","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":"75N93019C00077","grounded":true,"rationale":"The paper includes specific grant numbers from the National Institutes of Health and the Wellcome Trust. [majority verdict 'yes' (3/5 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":"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":"no","current":0.0,"evidence":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org ), CryptoDB (https://cryptodb.org ), FungiDB (https://fungidb.org ), GiardiaDB (https://giardiadb.org ), MicrosporidiaDB (https://microsporidiadb.org ), PiroplasmaDB (https://piroplasmadb.org ), PlasmoDB (https://plasmodb.org ), ToxoDB (https://toxodb.org ), TrichDB (https://trichdb.org ), TriTrypDB (https://tritrypdb.org ), VectorBase (https://vectorbase.org ), and VEuPathDB (https://veupathdb.org ).","why":"The paper provides URL addresses to the project websites but no persistent identifier (DOI, Handle, ARK, or repository accession) for the dataset. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":16.67,"priority":"essential","scored":true},{"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":"The paper does not state any license or reuse terms for the data; the Creative Commons license applies only to the article itself.","gain":16.67,"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":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org ), CryptoDB (https://cryptodb.org ), FungiDB (https://fungidb.org ), GiardiaDB (https://giardiadb.org ), MicrosporidiaDB (https://microsporidiadb.org ), PiroplasmaDB (https://piroplasmadb.org ), PlasmoDB (https://plasmodb.org ), ToxoDB (https://toxodb.org ), TrichDB (https://trichdb.org ), TriTrypDB (https://tritrypdb.org ), VectorBase (https://vectorbase.org ), and VEuPathDB (https://veupathdb.org ).","why":"The paper names VEuPathDB and its component projects as the holders of the data; VEuPathDB is a recognized bioinformatics resource center listed in re3data and FAIRsharing. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org ), CryptoDB (https://cryptodb.org ), FungiDB (https://fungidb.org ), GiardiaDB (https://giardiadb.org ), MicrosporidiaDB (https://microsporidiadb.org ), PiroplasmaDB (https://piroplasmadb.org ), PlasmoDB (https://plasmodb.org ), ToxoDB (https://toxodb.org ), TrichDB (https://trichdb.org ), TriTrypDB (https://tritrypdb.org ), VectorBase (https://vectorbase.org ), and VEuPathDB (https://veupathdb.org ).","why":"The paper provides a direct route to the data via the VEuPathDB project websites with no stated precondition such as registration, embargo, or application. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org ), CryptoDB (https://cryptodb.org ), FungiDB (https://fungidb.org ), GiardiaDB (https://giardiadb.org ), MicrosporidiaDB (https://microsporidiadb.org ), PiroplasmaDB (https://piroplasmadb.org ), PlasmoDB (https://plasmodb.org ), ToxoDB (https://toxodb.org ), TrichDB (https://trichdb.org ), TriTrypDB (https://tritrypdb.org ), VectorBase (https://vectorbase.org ), and VEuPathDB (https://veupathdb.org ).","why":"The dataset's identifier (URL) appears only in the body text of the data-availability statement, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper]","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":"partial","current":0.5,"evidence":"Project code can be found at our GitHub repository (https://github.com/VEuPathDB).","why":"The paper provides a URL to the project's GitHub repository for the code, which is a machine-resolvable locator. [downgraded to 'partial' — no verifiable quote from the paper]","gain":4.17,"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":"no","current":0.0,"evidence":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org), CryptoDB (https://cryptodb.org), FungiDB (https://fungidb.org), GiardiaDB (https://giardiadb.org), MicrosporidiaDB (https://microsporidiadb.org), PiroplasmaDB (https://piroplasmadb.org), PlasmoDB (https://plasmodb.org), ToxoDB (https://toxodb.org), TrichDB (https://trichdb.org), TriTrypDB (https://tritrypdb.org), VectorBase (https://vectorbase.org), and VEuPathDB (https://veupathdb.org).","why":"The statement points to the repository websites (general download tools) rather than a specific repository record with an accession or DOI. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Table 1. VEuPathDB resources and organisms supported ... Number of datasets (release 65) ... 3036","why":"The paper includes Table 1, which itemizes the VEuPathDB projects and the number of datasets, providing an inventory of the data. [downgraded to 'partial' — no verifiable quote from the paper] [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'. 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[downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Gene Ontology (GO) (3,4)","why":"The paper mentions the Gene Ontology, a community-standard ontology, as used for functional annotation of 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_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":"OrthoMCL","why":"The paper names a specific software tool (OrthoMCL) used in the data analysis pipeline. [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":"no","current":0.0,"evidence":"All data are available from the download tools on VEuPathDB project websites","why":"The paper does not mention a README, data dictionary, or codebook accompanying the data, nor does it include a table inside the article defining variables. [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":null,"why":"The paper does not discuss sensitive data or any gatekeeper for access; the data are from public domain sources and no access restrictions are mentioned.","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":"Sequence Read Archive (1) (https://www.ncbi.nlm.nih.gov/sra)","why":"The paper provides a URL and reference for the Sequence Read Archive, an external resource used by the study. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 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":"All data are available from the download tools on VEuPathDB project websites: AmoebaDB (https://amoebadb.org ), CryptoDB (https://cryptodb.org ), FungiDB (https://fungidb.org ), GiardiaDB (https://giardiadb.org ), MicrosporidiaDB (https://microsporidiadb.org ), PiroplasmaDB (https://piroplasmadb.org ), PlasmoDB (https://plasmodb.org ), ToxoDB (https://toxodb.org ), TrichDB (https://trichdb.org ), TriTrypDB (https://tritrypdb.org ), VectorBase (https://vectorbase.org ), and VEuPathDB (https://veupathdb.org ).","why":"The paper states that data are available now but does not specify how long they will persist, thus only an availability-timing statement is given. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["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).","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.","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":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:52:57.830282Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}