The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids is a dataset published in Nucleic Acids Research (2023). On theSindex it has a DataRank of 1.6, placing it in the top 13.1% of the data-sharing corpus. It has been cited 61 times, with 54 citing works in its 1-hop citation network. Its calibrated FAIR score is 29/100.
Ranks in the top 13% 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.
“nakb.org/download.html”
The only identifier for the dataset is a web URL, not a persistent identifier scheme such as DOI, Handle, 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'
“The Nucleic Acid Knowledgebase (nakb.org) is a new data resource”— not found in the paper; verdict downgraded
NAKB is a named host but is a custom database, not a repository listed in re3data/FAIRsharing with standard accessioning. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 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
“Data available for download from NAKB (nakb.org/download.html) include the NAKB accession id list (updated weekly), NAKB-assigned protein and NA functional and structural annotations (updated weekly), legacy NDB annotations, and coordinate files for 48 early structure entries not available in PDB.”— not found in the paper; verdict downgraded
The dataset identifier or link appears only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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
“Data available for download from NAKB (nakb.org/download.html) include the NAKB accession id list (updated weekly), NAKB-assigned protein and NA functional and structural annotations (updated weekly), legacy NDB annotations, and coordinate files for 48 early structure entries not available in PDB.”— not found in the paper; verdict downgraded
The statement points to a download page on a website, not a repository record with an accession or DOI. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 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
“Data available for download from NAKB (nakb.org/download.html) include the NAKB accession id list (updated weekly), NAKB-assigned protein and NA functional and structural annotations (updated weekly), legacy NDB annotations, and coordinate files for 48 early structure entries not available in PDB.”— not found in the paper; verdict downgraded
The dataset content is described in running prose as a list within a sentence, not as an itemised section, table, or bulleted list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 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'
“Data available for download from NAKB (nakb.org/download.html) include the NAKB accession id list (updated weekly), NAKB-assigned protein and NA functional and structural annotations (updated weekly), legacy NDB annotations, and coordinate files for 48 early structure entries not available in PDB.”— not found in the paper; verdict downgraded
The statement gives a direct download URL with no precondition or restriction. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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
“Data available for download from NAKB (nakb.org/download.html) include the NAKB accession id list (updated weekly), NAKB-assigned protein and NA functional and structural annotations (updated weekly), legacy NDB annotations, and coordinate files for 48 early structure entries not available in PDB.”— not found in the paper; verdict downgraded
The text describes the action of downloading data but does not label the access level with a standard vocabulary term. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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 structural annotations, not sensitive human-subject data, so no gatekeeper is needed or 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 paper states the website is updated weekly but does not state how long the data will persist or a retention period. [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'
“can be downloaded in excel, csv, and json formats”
The paper states that tabular reports can be downloaded in CSV format, which is an open, community-standard format. [majority verdict 'yes' (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
“Leontis-Westhof and Saenger basepair classifications”
The paper names the Leontis-Westhof basepair classification, a community standard for nucleic acid base pairs, as applied to the data. [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 7EZJ”
The paper provides identifiers for external resources (e.g., PDB IDs) that the data depend on.
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 only states a CC-BY license for the article, not for the data itself.
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'
The data are updated weekly but no version token or snapshot date 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'
The paper describes custom scripts but provides no locator (URL, DOI, or package identifier) for the 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)
“R01GM085328”
The paper includes a specific grant number from the 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
“DSSR”— not found in the paper; verdict downgraded
The paper names specific software (DSSR) used to produce annotations for 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
“Table 1. Data items for which searchable/sortable/downloadable data distributions can be obtained via the NAKB Annotation Tables Tool”
Variable definitions are provided inside the article in a table, not as a separate documentation object shipped with 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
0.619
From this paper's citation signal
Citation Network Contribution
0.967
From 34 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 54 citers.