VExD: a curated resource for human gene expression alterations following viral infection is a dataset published in G3 Genes Genomes Genetics (2023). On theSindex it has a DataRank of 0.241, placing it in the top 61.3% of the data-sharing corpus. It has been cited 4 times, with 2 citing works in its 1-hop citation network. Its calibrated FAIR score is 58/100.
Ranks in the top 61% for downstream scientific impact
DataRank reads this dataset's downstream impact straight off the citation graph — no black box, no proprietary weighting. How is this computed?
FAIR checklist signals are shown for context only and do not affect DataRank scoring.
Full FAIR picture · advisory
The headline score is computed from the scored criteria — the fact-shaped checks (a repository, an accession, a licence) that two independent models agree on. The advisory criteria below are real FAIR guidance but rest on judgment calls that models read differently, so they inform without moving the number.
“VExD is freely available at https://vexd.cchmc.org/ .”
The paper gives a web URL (https://vexd.cchmc.org) for the data, not a persistent identifier (DOI, Handle, ARK, or repository accession).
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'
“VExD is freely available at https://vexd.cchmc.org/ .”
The holder is a lab website (vexd.cchmc.org), not a curated repository listed in re3data/FAIRsharing. [majority verdict 'partial' (3/4 passes agreed)]
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
“VExD is freely available at https://vexd.cchmc.org/ .”
The dataset's identifier (URL) appears only in body text, not as a reference-list entry.
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'
Advisory · not in the published score
“Figure 2 and Supplementary Fig. 1 in this paper can be regenerated from the “Enrichment” tab of the website. Figure 5 can be regenerated from the “Genes” tab of the website. Supplementary File S1 contains a source code to recreate Fig. 3 . Supplementary File S2 contains a source code to recreate Fig. 4 . The genes used in Fig. 4a were the “genes of interest” from groups 1, 2, and 3 (upregulated upon infection) from Fig. 1 of ( Wang, Li et al . 2019 ). The genes used in Fig. 4b were similarly chosen from groups 7 and 8 of the same figure. Groups 4, 5, and 6 showed more complicated, time-dependent expression patterns and were thus not relevant for a simple “infected vs control” comparison. Supplementary Table 3 contains gene lists used in all figures. Supplemental material available at G3 online.”
The data availability statement points to the article and supplementary materials, not to a repository record. [majority verdict 'partial' (3/4 passes agreed)]
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
“VExD contains ∼8,000 uniformly processed samples obtained from 289 studies examining 51 distinct human viruses.”
The dataset's content is described in a prose sentence, not in an itemised inventory (section, table, or list).
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'
“The VExD website ( https://vexd.cchmc.org ) is freely available, with no registration required.”
The text gives a route with no precondition: the data are freely available now without any requirement. [majority verdict 'yes' (3/4 passes agreed)]
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'
Advisory · not in the published score
“The VExD website ( https://vexd.cchmc.org ) is freely available, with no registration required.”
The paper explicitly labels the data as freely available with no registration, which is an access-level label. [majority verdict 'yes' (3/4 passes agreed)]
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
“The VExD website ( https://vexd.cchmc.org ) is freely available, with no registration required.”
The data are not sensitive human-subject data, and no gatekeeper is named; the access is open.
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
No sentence states how long the data will remain available or any retention commitment.
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'
“Download links provide study and differential expression information in both a tab-delimited text file and a compressed, machine-readable format (Apache Parquet).”
The paper names tab-delimited text and Apache Parquet, both open, non-proprietary formats.
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
Advisory · not in the published score
“annotated with BRENDA tissue ontology (BTO) terms”
The paper uses a community-standard ontology (BTO) and Ensembl gene IDs, which are registered in FAIRsharing. [majority verdict 'yes' (3/4 passes agreed)]
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'
No specific identifier (accession, DOI, RRID) for a resource other than the paper's own dataset is quoted in the text.
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'
“This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/ )”
The only license mentioned is for the article, not for the dataset itself; no license is stated for the VExD data.
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'
No version token or date is given for the dataset itself; only the Ensembl reference version is mentioned, not the data snapshot.
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'
“Source code for the website is available at https://github.com/pdexheimer/vexd .”
A machine-resolvable code repository URL (GitHub) is provided for the study's own code.
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)
“This work was funded by the National Institutes of Health grants R01NS099068, R01HG010730, R01GM055479, U01AI130830, R01AI024717, U01AI150748, R01AI148276, and P01AI150585 to MTW.”
The paper includes specific NIH grant numbers alongside the funder name.
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
Advisory · not in the published score
“RNA-Seq samples were quantified using kallisto ( Bray et al . 2016 ) with the “--bias” parameter to account for sequence-specific biases.”
The paper names specific tools and versions used to produce the data. [majority verdict 'yes' (3/4 passes agreed)]
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
No documentation object is named either in the article or as accompanying the data. [majority verdict 'no' (3/4 passes agreed)]
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
Calibrated FAIR score — a parallel quality metric, independent of the DataRank citation score. See the full evaluation →
Base Score Contribution
0.241
From this paper's citation signal
Citation Network Contribution
0
From 0 citing papers with measurable signal
This paper's DataRank is currently driven only by its base citation score. None of the citing papers had measurable citation signal.
Learn more about DataRank methodology →National Institutes of Health
Grant: R01NS099068
National Institutes of Health
Grant: R01HG010730
National Institutes of Health
Grant: R01GM055479
National Institutes of Health
Grant: U01AI130830
National Institutes of Health
Grant: R01AI024717
National Institutes of Health
Grant: U01AI150748
National Institutes of Health
Grant: R01AI148276
National Institutes of Health
Grant: P01AI150585
NIAMS NIH HHS
Grant: P30 AR070549
National Institutes of Health
Grant: 5R01NS099068-08
Binding of Epstein Barr Virus EBNA2 Unifies Multiple Sclerosis Genetic Mechanisms
National Institutes of Health
Grant: 1P01AI150585-01A1
Molecular Mechanisms of the Dysregulated Immune Response to Ebola Virus
National Institutes of Health
Grant: 5R01GM055479-22
Biochemical and Computational Analysis of Notch signal transduction
National Institutes of Health
Grant: 1R01AI148276-01
Genomics of Inflammatory Bowel Disease
National Institutes of Health
Grant: 1U01AI150748-01
Dynamic regulatory network models of human response to influenza virus
National Institutes of Health
Grant: 5U01AI130830-05
Gene Regulation as a Foundation for Autoimmune Disease Prevention
National Institutes of Health
Grant: 2R01AI024717-04
HLA-DQ GENE COMPLEMENTATION IN LUPUS
National Institutes of Health
Grant: 5R21HG008186-02
Effect of disease-associated genetic variants on viral protein DNA binding
National Institutes of Health
Grant: 5R01HG010730-03
Virus-driven human gene misregulation in disease
FWCI
0.36
Citation Percentile
0.5%
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals