RegulonDB v12.0: a comprehensive resource of transcriptional regulation inE. coliK-12 is a dataset published in Nucleic Acids Research (2023). On theSindex it has a DataRank of 1.9, placing it in the top 11.3% of the data-sharing corpus. It has been cited 113 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 71/100.
Ranks in the top 11% 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.
“DOI 10.5281/zenodo.8346680”
The paper provides a DOI for the dataset, which is a persistent identifier scheme. [majority verdict 'yes' (3/5 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'
“Zenodo”
The data are deposited in Zenodo, a recognised data repository. [majority verdict 'yes' (3/5 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
“DOI 10.5281/zenodo.8346680”
The dataset identifier appears only in the body text of the Data availability section, not in the reference list. [majority verdict 'partial' (3/5 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
“All RegulonDB programs are available as open source under Apache License 2.0 license. Users can access them in the RegulonDB software project repository on GitHub at the following link: https://github.com/regulondbunam/regulondb-releases/ . This license allows users to use, modify, and share the code openly as long as it is properly attributed to RegulonDB. The release data version 12.0 of RegulonDB have been registered in Zenodo with DOI 10.5281/zenodo.8346680 and the entire code is in FigShare with DOI 10.6084/m9.figshare.24129402.”
The data availability statement points to a repository record (Zenodo, FigShare) with DOIs, fitting Colavizza category 3. [majority verdict 'yes' (3/5 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
“The total number of current objects and the total increase of objects compared to version 10.5 are shown in Table 1.”— not found in the paper; verdict downgraded
Table 1 provides an itemised inventory of the dataset's objects (promoters, RIs, etc.). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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'
“The release data version 12.0 of RegulonDB have been registered in Zenodo with DOI 10.5281/zenodo.8346680”
The text gives a direct route to the data in a public repository without any stated precondition. [majority verdict 'yes' (3/5 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
“The current version of RegulonDB's data has been registered in Zenodo with their citation and a permanent link to this version, thus guaranteeing their findability and accessibility.”— not found in the paper; verdict downgraded
The paper describes the action of registering the data in Zenodo but does not apply an explicit access-level label such as 'open access' or 'publicly available'. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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 or human-subject, 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
“The current version of RegulonDB's data has been registered in Zenodo with their citation and a permanent link to this version, thus guaranteeing their findability and accessibility.”— not found in the paper; verdict downgraded
The paper claims a permanent link and registration in Zenodo, implying a persistence commitment. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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'
No file format for the released data is named in the text. [majority verdict 'no' (4/5 passes agreed)]
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
“ECO ontology”
The paper names the ECO ontology, Gene Ontology, and Microbial Conditions Ontology as community standards applied to the data. [majority verdict 'yes' (3/5 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'
“U00096.3”— not found in the paper; verdict downgraded
The paper uses the genome version U00096.3, an identifier for an external resource (the E. coli genome assembly). [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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'
The paper names the Apache License 2.0 for code but does not name a licence for 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'
“version 12.0”
The paper explicitly states the version number of the data. [majority verdict 'yes' (3/5 passes agreed)]
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/regulondbunam/regulondb-releases/”
The paper provides a GitHub repository URL and a FigShare DOI for the code. [majority verdict 'yes' (3/5 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)
“GM077678”
The paper lists specific grant numbers from NIH. [majority verdict 'yes' (3/5 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
“ChIP-seq”— not found in the paper; verdict downgraded
The paper names specific high-throughput methods used to generate 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 mentioned as travelling with the data, nor is there a variable-definition table inside the article. [majority verdict 'no' (3/5 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
0.710
From this paper's citation signal
Citation Network Contribution
1.2
From 53 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 100 citers.
National Institute of General Medical Sciences
Grant: GM077678
National Institute of General Medical Sciences
Grant: 5RO1GM131643
NIGMS NIH HHS
Grant: R01 GM131643
NIGMS NIH HHS
Grant: U24 GM077678
NIGMS NIH HHS
Grant: R01 GM077678
National Institutes of Health
Grant: 5R01GM077678-29
The EcoCyc Model Organism Database for Escherichia coli
National Institutes of Health
Grant: 5R01GM131643-03
A Comprehensive Resource for Escherichia coli Genomic Data and Tools
Universidad Nacional Autónoma de México
NIH HHS
National Institutes of Health
Sistema Nacional de Investigadores
Dirección General de Asuntos del Personal Académico—Universidad Nacional Autónoma de México
NIH HHS
FWCI
10.52
Citation Percentile
1.0%
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals