DNAproDB: an updated database for the automated and interactive analysis of protein–DNA complexes is a dataset published in Nucleic Acids Research (2024). On theSindex it has a DataRank of 0.848, placing it in the top 23.7% of the data-sharing corpus. It has been cited 38 times, with 33 citing works in its 1-hop citation network. Its calibrated FAIR score is 52/100.
Ranks in the top 24% 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.
“DNAproDB and associated data are freely available for all users at https://dnaprodb.usc.edu/”
The strongest identifier for the dataset is a URL (https://dnaprodb.usc.edu/), not a PID scheme. The DOI is for the code, not the data. [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'
“DNAproDB and associated data are freely available for all users at https://dnaprodb.usc.edu/”
The data are held at the DNAproDB website, which is a non-repository host (not a curated archive listed in re3data/FAIRsharing). [majority verdict 'partial' (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
“DNAproDB and associated data are freely available for all users at https://dnaprodb.usc.edu/”
The dataset identifier (URL) appears only in body text (data availability statement), 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
“DNAproDB and associated data are freely available for all users at https://dnaprodb.usc.edu/ . The pipeline and frontend implementations are available through figshare at https://doi.org/10.6084/m9.figshare.27263145 , and via GitHub at https://github.com/timkartar/DNAproDB and https://github.com/ariscohen/DNAproDB_frontend .”
The data availability statement points to a URL (website) for the data, not a repository record, so it is category 3 but the data part is not a repository record; thus partial. [majority verdict 'partial' (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
“The latest collection size as of 7 June 2024, is 6731 structures.”
The paper gives the dataset's size in a running prose sentence, not in an itemised inventory or section heading.
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'
“DNAproDB and associated data are freely available for all users at https://dnaprodb.usc.edu/”
The text gives a route to the data with no stated precondition; the data are stated to be freely available. [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
“DNAproDB and associated data are freely available for all users at https://dnaprodb.usc.edu/”
The paper states that the data are 'freely available', which is an explicit access-level label equivalent to 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 not sensitive or 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
“DNAproDB and associated data are freely available for all users at https://dnaprodb.usc.edu/”
The paper states that the data are freely available now but does not specify how long they will persist, so it is an availability-timing statement only. [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' (3/5 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
“Atomic resolution structures of protein–DNA complexes available in the Protein Data Bank (PDB)”
The paper names the Protein Data Bank (PDB) as a community standard for the data, which is a data/metadata standard. [majority verdict 'yes' (4/5 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'
“PDB ID: 1TRO”
The paper gives identifiers (PDB IDs) for structures that the data depend on or derive from.
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-NC 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'
“as of 7 June 2024”
A date pins the snapshot of the data, but no version token is given.
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://doi.org/10.6084/m9.figshare.27263145”
The code is available via a figshare DOI and GitHub URLs, which are machine-resolvable locators.
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)
“R35GM130376”
The paper gives an award number (R35GM130376) from a named funder (NIH).
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
“HBPLUS”— not found in the paper; verdict downgraded
The paper names a specific tool (HBPLUS) used to produce the data annotations. [downgraded to 'partial' — no verifiable quote from the paper]
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, codebook) is named as accompanying the data. [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
0.550
From this paper's citation signal
Citation Network Contribution
0.299
From 17 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 33 citers.
National Institutes of Health
Grant: R35GM130376
Human Frontier Science Program
Grant: RGP0021/2018
National Institutes of Health
Grant: 5R35GM130376-03
Quantitative Modeling of Transcription Factor-DNA Binding
Andrew J. Viterbi Fellowship
Fields of Study
MeSH Terms
Keywords