A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees is a dataset published in Molecular Biology and Evolution (2021). On theSindex it has a DataRank of 3.8, placing it in the top 6% of the data-sharing corpus. It has been cited 121 times, with 81 citing works in its 1-hop citation network. Its calibrated FAIR score is 27/100.
Ranks in the top 6% for downstream scientific impact
Linked data & code
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.
“Our daily-updated SARS-CoV-2 MAT database and matUtils software are available at http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/”— not found in the paper; verdict downgraded
The only identifier given is a web URL, not a persistent identifier scheme. [downgraded to 'no' — no verifiable quote from the paper]
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'
“Our daily-updated SARS-CoV-2 MAT database and matUtils software are available at http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/”— not found in the paper; verdict downgraded
The data is hosted on a UCSC server, which is a non-repository host. [downgraded to 'no' — no verifiable quote from the paper]
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
“Our daily-updated SARS-CoV-2 MAT database and matUtils software are available at http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/”— not found in the paper; verdict downgraded
The dataset's identifier URL appears only in the body text, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper]
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
“Data Availability Our daily-updated SARS-CoV-2 MAT database and matUtils software are available at http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/ and https://github.com/yatisht/usher, respectively.”— not found in the paper; verdict downgraded
The statement points to a web link, not a repository record with an accession or DOI. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 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
“our SARS-CoV-2 MAT consists of 834,521 sequences and provides a comprehensive view of the virus’ evolutionary history using public data.”
The dataset is described in running prose without an itemised inventory of files or variables.
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'
“Our daily-updated SARS-CoV-2 MAT database and matUtils software are available at http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/ and https://github.com/yatisht/usher, respectively.”— not found in the paper; verdict downgraded
The data is accessible via a URL with no stated precondition such as registration, embargo, or request. [downgraded to 'partial' — no verifiable quote from the paper]
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
“openly sharing a daily-updated database of mutation-annotated trees (MATs) containing global SARS-CoV-2 sequences from public databases”
The paper explicitly labels the data as 'openly shared', which is a natural-language equivalent of 'open access'. [majority verdict 'yes' (4/5 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 data are viral sequences, not human-subject or sensitive, and no gatekeeper is named.
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
“Our daily-updated SARS-CoV-2 MAT database and matUtils software are available at ...”— not found in the paper; verdict downgraded
The paper states the data are available now but provides no commitment to how long they will persist. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]
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'
“mutation-annotated tree (MAT) format”
The MAT format is not listed among the open community-standard formats provided in the rubric.
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
“including annotations for Nextstrain clades (Hadfield et al. 2018) and Pango lineages (Rambaut et al. 2020; supplementary fig. 1)”— not found in the paper; verdict downgraded
Nextstrain clades and Pango lineages are community standards for naming SARS-CoV-2 variants. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 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'
“Wuhan/Hu-1 (GenBank MN908947.3, RefSeq NC_045512.2)”
The paper provides GenBank and RefSeq identifiers for the reference genome, which is a resource other than the study's own data.
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'
No licence artefact is named for the data; the CC BY-NC licence applies to the article, not the 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'
“As of June 9, 2021, our MAT consists of 834,521 sequences”
The snapshot is identified by a date, not a version token.
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'
“https://github.com/yatisht/usher”
A machine-resolvable code repository URL is provided for the study's own software. [majority verdict 'yes' (4/5 passes agreed)]
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)
“R35GM128932”
The paper includes a specific grant number (R35GM128932) in the acknowledgments, attached to a named funder.
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
“we have set up an automated pipeline to aggregate public sequences available through GenBank, COG-UK, and the China National Center for Bioinformation on a daily basis and incorporate them into our MAT using UShER”— not found in the paper; verdict downgraded
The paper names specific tools and databases (UShER, GenBank, COG-UK) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 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 (e.g., README, codebook) is named as travelling with the deposited data.
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
0.721
From this paper's citation signal
Citation Network Contribution
3.0
From 68 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 81 citers.
Alfred P. Sloan Foundation fellowship
Grant: R35GM128932
Alfred P. Sloan Foundation fellowship
Grant: T32HG008345
Alfred P. Sloan Foundation fellowship
Grant: F31HG010584
NHGRI
Grant: 5U41HG002371
CDC
Grant: BAA 200-2021-11554
Schmidt Futures Foundation
Grant: SF 857
NIH
Grant: 5R01HG010485
NHGRI NIH HHS
Grant: U41 HG002371
NHGRI NIH HHS
Grant: R01 HG010485
National Institutes of Health
Grant: 1F31HG010584-01
Evolutionary dynamics of tRNA genes
National Institutes of Health
Grant: 1R01HG010485-01A1
Enabling Comparative Pangenomics
National Institutes of Health
Grant: 1T32HG008345-01
UC Santa Cruz Training Program In Genomic Sciences
National Institutes of Health
Grant: 1R35GM128932-01
Genetic variation, admixture and genome structure evolution through the lense of Drosophila genomics
National Institutes of Health
Grant: 5U41HG002371-21
The UCSC Genome Browser
Eric
Schmidt Futures program
Wendy Schmidt
European Molecular Biology Laboratory
FWCI
5.70
Citation Percentile
1.0%
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals