Average nucleotide identity-based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome is a dataset published in mSystems (2024). On theSindex it has a DataRank of 0.688, placing it in the top 29.1% of the data-sharing corpus. It has been cited 16 times, with 10 citing works in its 1-hop citation network. Its calibrated FAIR score is 58/100.
Ranks in the top 29% 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.
“PIRATE pangenome outputs, genes and strain lists, and representative genome sets are available on Zenodo ( https://zenodo.org/records/10471309 ).”
The identifier is a web URL (https://zenodo.org/records/10471309) not in a PID scheme; Zenodo records have DOIs but the paper does not quote the DOI string. [majority verdict 'partial' (4/5 passes agreed)]
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'
“PIRATE pangenome outputs, genes and strain lists, and representative genome sets are available on Zenodo ( https://zenodo.org/records/10471309 ).”
Zenodo is a named data repository. [majority verdict 'yes' (4/5 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
“PIRATE pangenome outputs, genes and strain lists, and representative genome sets are available on Zenodo ( https://zenodo.org/records/10471309 ).”
The dataset identifier (Zenodo URL) appears only in the body text, not in the reference list. [majority verdict 'partial' (4/5 passes agreed)]
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
“PIRATE pangenome outputs, genes and strain lists, and representative genome sets are available on Zenodo ( https://zenodo.org/records/10471309 ).”
The statement points to a repository record on Zenodo, a public repository. [majority verdict 'yes' (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
“PIRATE pangenome outputs, genes and strain lists, and representative genome sets are available on Zenodo ( https://zenodo.org/records/10471309 ).”
The dataset's content is described in running prose without an itemized inventory. [majority verdict 'partial' (4/5 passes agreed)]
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'
“PIRATE pangenome outputs, genes and strain lists, and representative genome sets are available on Zenodo ( https://zenodo.org/records/10471309 ).”
The data are stated to be available on Zenodo without any precondition. [majority verdict 'yes' (4/5 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
“PIRATE pangenome outputs, genes and strain lists, and representative genome sets are available on Zenodo ( https://zenodo.org/records/10471309 ).”
The paper states the data are available on Zenodo, describing an action to obtain the data without explicitly labeling the access level. [majority verdict 'partial' (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 not sensitive human-subject data; no gatekeeper is mentioned.
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 addresses when the data are available or how long they persist.
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'
No file format is named for the released data.
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
No data or metadata community standard is named.
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'
“A ST93 strain (accession number GCA_000144955.2) was drawn at the root as described in ( 20 ).”— not found in the paper; verdict downgraded
An accession number (GCA_000144955.2) is given for a reference genome, a resource other than the paper's own dataset. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]
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 license is named for the data; the article's CC-BY 4.0 license applies to the paper, 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'
No version token or date is given for 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'
“R code for generating figures can be found in https://github.com/VishnuRaghuram94/SCAPE .”
A machine-resolvable GitHub URL is given for the code. [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)
“T.D.R. was supported by funding from National Institutes of Health (NIH) awards AI158452 and AI139188.”
Award numbers (AI158452, AI139188) are provided with named funders. [majority verdict 'yes' (4/5 passes agreed)]
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
“Bactopia v.1.7.0 was used to download and process all genomes used in this data set.”
A specific tool and version are named for data production. [majority verdict 'yes' (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 (README, data dictionary) is stated to accompany the 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
0.425
From this paper's citation signal
Citation Network Contribution
0.263
From 7 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 10 citers.
HHS | National Institutes of Health
Grant: AI139188
HHS | National Institutes of Health
Grant: AI138952
HHS | National Institutes of Health
Grant: AI158452
Simons Foundation
Grant: 508600
Alfred P. Sloan Foundation
Grant: FG-2021-16667
National Science Foundation
Grant: 2146260
CAREER: Quantifying Adaptation and Recombination in Pathogen Populations
NIAID NIH HHS
Grant: R01 AI158452
NIAID NIH HHS
Grant: T32 AI138952
NIAID NIH HHS
Grant: R01 AI139188
National Institutes of Health
Grant: 5R01AI158452-03
Staphylococcus aureus SPREAD (S. aureus Study of Prevalence Resistance and Environmental Dissemination)
National Institutes of Health
Grant: 5R01AI139188-05
Genomics of S. Aureus Colonization after Initial and Recurrent Skin Infections and the Impact of Antibiotics
National Institutes of Health
Grant: 5T32AI138952-02
Infectious Diseases Across Scales Training Program
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals