Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 Epidemic is a dataset published in Molecular Biology and Evolution (2021). On theSindex it has a DataRank of 2.3, placing it in the top 9.1% of the data-sharing corpus. It has been cited 36 times, with 34 citing works in its 1-hop citation network. Its calibrated FAIR score is 54/100.
Ranks in the top 9% 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.
“The deleted SRA files recovered from the Google Cloud are all available at https://github.com/jbloom/SARS-CoV-2_PRJNA612766/tree/main/results/sra_downloads .”
The identifier is a web URL (GitHub), not a persistent identifier scheme such as DOI, Handle, or a repository accession. [majority verdict 'partial' (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'
“The deleted SRA files recovered from the Google Cloud are all available at https://github.com/jbloom/SARS-CoV-2_PRJNA612766/tree/main/results/sra_downloads .”
GitHub is named as the host, but it is not a curated data repository in the sense of the class 1 list. [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
“The deleted SRA files recovered from the Google Cloud are all available at https://github.com/jbloom/SARS-CoV-2_PRJNA612766/tree/main/results/sra_downloads .”
The dataset identifier (URL) appears only in the body text, not in the reference list. [majority verdict 'partial' (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
“The computer code and input data necessary to reproduce all analyses described in this paper are available on GitHub at https://github.com/jbloom/SARS-CoV-2_PRJNA612766 . This GitHub repository includes a Snakemake ( Mölder et al. 2021 ) pipeline that fully automates all steps in the analysis except for downloading the sequences from GISAID, which must be done manually as described in the GitHub repository’s README to comply with GISAID data sharing terms. The deleted SRA files recovered from the Google Cloud are all available at https://github.com/jbloom/SARS-CoV-2_PRJNA612766/tree/main/results/sra_downloads . I have suffixed the file extension.sra to all these files. The consensus sequences recovered from these deleted SRA files are linked to in the relevant subsection.”
The statement points to a GitHub repository containing the data, which is a public repository with a link. [majority verdict 'yes' (3/5 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
“These consensus sequences over the entire SARS-CoV-2 genome are available at https://github.com/jbloom/SARS-CoV-2_PRJNA612766/raw/main/results/consensus/consensus_seqs.csv ; note that they are mostly N nucleotides since the sequencing approach of Wang et al. (2020) only covers part of the genome.”— not found in the paper; verdict downgraded
The dataset content is described in running prose (a sentence stating what the file contains), not in an itemised list or section. [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'
“The deleted SRA files recovered from the Google Cloud are all available at https://github.com/jbloom/SARS-CoV-2_PRJNA612766/tree/main/results/sra_downloads .”
The data are available at a GitHub URL with no stated precondition such as registration, embargo, or application. [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
“The deleted SRA files recovered from the Google Cloud are all available at https://github.com/jbloom/SARS-CoV-2_PRJNA612766/tree/main/results/sra_downloads .”
The paper describes where the data can be downloaded but does not use an explicit access-level label such as 'open access' or 'publicly available'. [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 samples were from human subjects, but the paper does not name any gatekeeper for access to the recovered data.”— not found in the paper; verdict downgraded
No gatekeeper is named; the data are openly available on GitHub with no stated access restrictions.
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
Neither the timing nor the persistence of the data availability is addressed in any sentence.
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'
“I have suffixed the file extension.sra to all these files.”
The released data are in SRA format (.sra), which is a proprietary format, not an open community standard. [majority verdict 'partial' (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
No data or metadata community standard (e.g., MIAME, ISA-Tab, ontology) is named for the 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 majority of entries in this table refer to a project (BioProject PRJNA612766) by Wuhan University”
The paper provides an identifier (BioProject PRJNA612766) for the deleted project, which is a resource other than the study's own data. [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 license for the data is mentioned in the text; the article's CC BY license does not apply to 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'
No version token or date is given for the dataset. [majority verdict 'no' (3/5 passes agreed)]
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 computer code and input data necessary to reproduce all analyses described in this paper are available on GitHub at https://github.com/jbloom/SARS-CoV-2_PRJNA612766 .”
A machine-resolvable locator (GitHub URL) is provided for the code. [majority verdict 'yes' (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)
“S10OD028685”
A grant number (S10OD028685) is provided along with a funder (NIH). [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
“I used the SRA Toolkit to get the object timestamp (vdb-dump –obj_timestamp) and time (vdb-dump –info) for all SRA files.”
The paper names specific tools (SRA Toolkit, minimap2, etc.) used to process the data. [majority verdict 'yes' (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
“Table 1. Samples for which the SARS-CoV-2 sequence could be called at ≥ 90% of sites between 21,570 and 29,550, and the substitutions in this region relative to the putative SARS-CoV-2 progenitor proCoV2 inferred by Kumar et al. (2021).”— not found in the paper; verdict downgraded
Variable-level definitions (samples, substitutions) are provided inside the article's Table 1, not in a separate documentation file shipped with the data. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 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
0.542
From this paper's citation signal
Citation Network Contribution
1.8
From 30 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 34 citers.
NIH
Grant: S10OD028685
National Institutes of Health
Grant: 1S10OD028685-01
High-Performance Compute Cluster for Comprehensive Cancer and Infectious Diseases Research
Howard Hughes Medical Institute
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals