Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures is a dataset published in Scientific Data (2024). On theSindex it has a DataRank of 0.571, placing it in the top 34.4% of the data-sharing corpus. It has been cited 19 times, with 11 citing works in its 1-hop citation network. Its calibrated FAIR score is 77/100.
Ranks in the top 34% 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.
“https://doi.org/10.7910/DVN/FCDG0W”
The paper provides a DOI for the dataset.
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'
“Harvard Dataverse”
The paper names Harvard Dataverse as the repository holding the data.
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
“Giri, N., Wang, L. & Cheng, J. Cryo2StructData: Full Dataset https://doi.org/10.7910/DVN/FCDG0W (2023).”
The dataset appears 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 Cryo2StructData Dataverse comprises the Full Cryo2StructData, referred to as Cryo2StructData: Full Dataset 13 (https://doi.org/10.7910/DVN/FCDG0W), along with its associated trained deep transformer model and data splits, referred as Cryo2StructData: Trained Model and Data Splits (Full) 34 (https://doi.org/10.7910/DVN/SXNYRE).”
The statement points to a repository record with a DOI.
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 following data files for each cryo-EM density map are provided in its individual directory:”
The paper includes an itemized inventory of the dataset contents. [majority verdict 'yes' (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'
“we published all data to the Harvard Dataverse (https://dataverse.harvard.edu/dataverse/Cryo2StructData), an online data management and sharing platform with a permanent Digital Object Identifier number for each dataset.”
The data are deposited in a public repository with no stated precondition.
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
“Cryo2StructData is the first, large, publicly available cryo-EM dataset with standardized input features and well-curated output labels”
The paper labels the data as 'publicly available', which is a natural-language equivalent of 'open access'. [majority verdict 'yes' (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
“we published all data to the Harvard Dataverse (https://dataverse.harvard.edu/dataverse/Cryo2StructData)”
The data are not human-subject or sensitive; 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
No statement about retention period or persistence of the data. [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'
“The experimental cryo-EM density maps are stored in MRC26 format.”
MRC is an open, community-standard format for cryo-EM 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
“compliance with the MRC2014 format specification 26”
The paper names MRC2014, a community standard file format for cryo-EM, which is a data standard, class 1 (yes). [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'
“https://github.com/BioinfoMachineLearning/cryo2struct”— not found in the paper; verdict downgraded
The paper provides a URL for the code repository, which is an identifier for a resource other than the dataset. [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 is stated 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 version released as of March 2023”
A date is given for the dataset version.
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'
“freely available at https://github.com/BioinfoMachineLearning/cryo2struct”— not found in the paper; verdict downgraded
A machine-resolvable code repository URL is provided. [downgraded to 'partial' — no verifiable quote from the paper]
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)
“R01GM146340 and R01GM093123”
NIH grant numbers are provided.
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
“using vol resample command within UCSF ChimeraX27 in the non-interactive mode.”
The paper names specific tools used in data production.
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
“A comprehensive documentation of the Cryo2StructData is available within the Cryo2StructData Dataverse13,31,34,35.”
Documentation is stated to accompany the data in the repository.
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
0.449
From this paper's citation signal
Citation Network Contribution
0.122
From 6 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 11 citers.
NIGMS NIH HHS
Grant: R01 GM093123
NIGMS NIH HHS
Grant: R01 GM146340
National Science Foundation
Grant: 2308699
Deep transformers for integrating protein sequence, structure and interaction data to predict function
National Institutes of Health
Grant: 5R01GM093123-10
Distance-based ab initio protein structure prediction
National Institutes of Health
Grant: 5R01GM146340-03
Deep learning methods for automated and accurate reconstruction of protein structures from cryo-EM image data
Fields of Study
MeSH Terms
Keywords
Cryo2StructData : Full Dataset