eLife Assessment: DNA methylation-environment interactions in the human genome is a dataset (2024). On theSindex it has a DataRank of 0, placing it in the top 100% of the data-sharing corpus. Its calibrated FAIR score is 67/100.
Ranks in the top 100% 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.
“mSTARR-seq RNA and DNA sequencing data generated in this study for K562 and HepG2 cells are available in the NCBI Sequence Read Archive (SRA; BioProject accession number PRJNA922490). K562 endogenous RNA-seq data are available in the NCBI Gene Expression Omnibus (GEO series accession GSE222643).”
The paper provides BioProject (PRJNA922490) and GEO (GSE222643) accessions, which are persistent identifier schemes.
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'
“mSTARR-seq RNA and DNA sequencing data generated in this study for K562 and HepG2 cells are available in the NCBI Sequence Read Archive (SRA; BioProject accession number PRJNA922490). K562 endogenous RNA-seq data are available in the NCBI Gene Expression Omnibus (GEO series accession GSE222643).”
The paper names NCBI SRA and NCBI GEO, both curated repositories listed in re3data.
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
“mSTARR-seq RNA and DNA sequencing data generated in this study for K562 and HepG2 cells are available in the NCBI Sequence Read Archive (SRA; BioProject accession number PRJNA922490). K562 endogenous RNA-seq data are available in the NCBI Gene Expression Omnibus (GEO series accession GSE222643).”
The identifier appears only in the body text (Data Availability section), 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
“mSTARR-seq RNA and DNA sequencing data generated in this study for K562 and HepG2 cells are available in the NCBI Sequence Read Archive (SRA; BioProject accession number PRJNA922490). K562 endogenous RNA-seq data are available in the NCBI Gene Expression Omnibus (GEO series accession GSE222643).”
The data-availability statement points to repository records with accessions (Colavizza category 3). [majority verdict 'yes' (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
“We assessed regulatory activity and methylation-dependent regulatory activity for 4,558,475 600-base pair windows of the genome by pairing hybridization capture of targeted loci in the human genome with the massively parallel reporter assay, mSTARR-seq (Lea et al., 2018).”— not found in the paper; verdict downgraded
The dataset's extent is described in running prose but no itemised inventory (section, table, or list) is given. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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'
“mSTARR-seq RNA and DNA sequencing data generated in this study for K562 and HepG2 cells are available in the NCBI Sequence Read Archive (SRA; BioProject accession number PRJNA922490).”
The data are placed in public repositories (NCBI SRA, GEO) with no stated precondition for access.
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
“mSTARR-seq RNA and DNA sequencing data generated in this study for K562 and HepG2 cells are available in the NCBI Sequence Read Archive (SRA; BioProject accession number PRJNA922490).”
The paper states the data are available in repositories but does not apply an explicit access-level label like 'open access'. [majority verdict 'partial' (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 study's own data are from cell lines, not human subjects, so 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 sentence states how long the data will persist or when they become available beyond the current availability.
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 (e.g., FASTQ, BED) for the released 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
No community data or metadata standard (e.g., MIAME, MINSEQE, an ontology) is named for the released data.
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'
“The previously published data from (Lea et al., 2018 ) used in this study are available in NCBI’s SRA accession number SRP120556.”
The paper provides an identifier (SRP120556) for a resource (Lea et al. 2018 dataset) other than its own. [majority verdict 'yes' (4/5 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 reuse licence is stated for the data; only the article's CC BY licence is mentioned.
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'
No version token or date is provided to identify a specific snapshot of the data.
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 zenodo repository at https://zenodo.org/record/7949036#.ZGZ5UnbMJq9 provides the code used for analyses, as well as track files (compatible with the UCSC genome browser) for mSTARR-seq hg38 windows with regulatory activity, and windows with methylation-dependent regulatory activity, in all three conditions (baseline, IFNA, and dex).”
A Zenodo DOI provides a machine-resolvable, versioned locator for the study's 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)
“This study was supported by the National Institutes of Health (R01HD088558 to J.T. and F32HD095616 to R.A.J.)”
The paper provides specific grant numbers (R01HD088558, F32HD095616) attached to named funders. [majority verdict 'yes' (4/5 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
“mSTARR RNA-seq and DNA-seq libraries were sequenced on the Illumina NovaSeq platform as 100 basepair, paired-end reads.”— not found in the paper; verdict downgraded
The paper names the specific sequencing platform (Illumina NovaSeq) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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 (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 →