De novo3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures is a dataset published in Nucleic Acids Research (2021). On theSindex it has a DataRank of 2.8, placing it in the top 7.8% of the data-sharing corpus. It has been cited 85 times, with 81 citing works in its 1-hop citation network. Its calibrated FAIR score is 58/100.
Ranks in the top 8% 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.
“Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab).”
The paper provides RMDB accession numbers for the chemical probing data, which are persistent identifiers issued by a curated repository. [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'
“Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab).”
RMDB is named as the repository for chemical probing data; RMDB is a data repository listed in re3data, fulfilling the 'yes' class. [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
“Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab).”
The dataset identifiers (RMDB accessions, GitHub URLs, PURL) appear only in the body text (Data Availability section) and not as a reference-list entry.
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
“The supplementary file includes depictions of top-scoring cluster centers for the full extended 5′ UTR, the extended FSE with alternative secondary structures, the FSE dimer, the full 3′ UTR, the hypervariable region and an extended 3′ UTR pseudoknot construct modeled with both the BSL and extended pseudoknot secondary structures. Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab). FARFAR2-SARS-CoV-2 models are included at https://github.com/DasLab/FARFAR2-SARS-CoV-2 . FARFAR2-Apo-Riboswitch models are included at https://github.com/DasLab/FARFAR2-Apo-Riboswitch . Pocket predictions are included in the Github repositories. Large model sets, comprising the top 5% of models for each simulation as ranked by Rosetta score, are included at the PURL repository https://purl.stanford.edu/pp620tj8748 .”
The data availability statement points to multiple public repositories (RMDB, GitHub, PURL) with accessions and URLs, corresponding to Colavizza category 3 (link to archived data in a public repository).
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
“Table 1. FARFAR2-SARS-CoV-2 models”
The paper includes a structured table (Table 1) that lists the modeled systems, lengths, and generation metrics, providing an itemised inventory of the dataset.
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'
“Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab).”
The data availability statement gives URLs to RMDB, GitHub, and a PURL without any precondition such as embargo, registration, or application; the data are stated to be available now.
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
“Chemical probing data collected in this study are available on RMDB (entries: FWSL14_UTR_0003 for SL1–4 in the 5′ UTR, FWSL26_UTR_0002 for SL2–6 in the 5′ UTR, RCSL14_UTR_0003 for the reverse complement of SL1–4 in the 5′ UTR, HVRS2M_UTR_0003 for the hyper-variable region in the 3′ UTR, and SHAPE_RYOS_0620 for the Eterna Roll Your Own Structure Lab).”
The paper states the data are available on RMDB and GitHub, which describes the access action but does not apply an explicit access-level label such as 'open access' or 'freely available'. [majority verdict 'partial' (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 human-subject data, and no gatekeeper is named; the criterion is not applicable, so the verdict is 'no'.
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 does not mention any retention period, persistence commitment, or timing of availability beyond the current availability statement.
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'
The paper does not name any file format (open or proprietary) for the released data; only the term 'models' is used without specifying a format token.
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 (e.g., MIAME, FAIRsharing-registered ontology) is named for the data; only manuscript reporting guidelines are absent.
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'
“For the 5′ UTR SL2, PDB ID 2L6I (11) was used as a template for positions 45–59.”— not found in the paper; verdict downgraded
The paper cites PDB IDs (2L6I, 1XJR) for external structural templates used in homology modeling. [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'
No license or terms-of-use document is named for the data; the CC-BY license applies only 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'
Neither a version token nor a date is provided to identify which snapshot of the data was released; the data are referred to without versioning.
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 does not provide a locator for the study's own code; it only mentions third-party software (HiTRACE, Biers, Rosetta) without offering the custom scripts used. [majority verdict 'no' (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)
“National Institutes of Health [R21 AI145647, R35 GM122579]”
The paper includes award/grant numbers (e.g., NIH R21 AI145647, R35 GM122579) attached to named funders, meeting the 'yes' class.
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
“The models were created using the rna_denovo application in Rosetta 3.12 using default parameters for FARFAR2”
The paper names specific software (Rosetta 3.12, FARFAR2) and instruments (Miseq, T7 TranscriptAid kits) used to produce the data, fulfilling the 'yes' class.
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
“The supplementary file includes depictions of top-scoring cluster centers for the full extended 5′ UTR, the extended FSE with alternative secondary structures, the FSE dimer, the full 3′ UTR, the hypervariable region and an extended 3′ UTR pseudoknot construct modeled with both the BSL and extended pseudoknot secondary structures.”
Variable-level definitions are provided within the article (supplementary file) rather than in a separate documentation object shipped with the data. [majority verdict 'partial' (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
0.668
From this paper's citation signal
Citation Network Contribution
2.2
From 72 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.
National Science Foundation
Grant: DGE-1656518
National Institutes of Health
Grant: R21 AI145647
National Institutes of Health
Grant: R35 GM122579
National Science Foundation
Grant: 2030508
Partnership to Advance Throughput Computing (PATh)
NCI NIH HHS
Grant: R21 CA219847
National Institutes of Health
Grant: 5R21AI145647-02
Structural interrogation of the HIV-1 5′ leader RNA by multidimensional chemical mapping and cryoelectron microscopy
National Institutes of Health
Grant: 1R35GM122579-01
Next-generation computational/chemical methods for complex RNA structures
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals