Escherichia coli transcriptome assembly from a compendium of RNA-seq data sets is a dataset published in RNA Biology (2023). On theSindex it has a DataRank of 0.417, placing it in the top 44.4% of the data-sharing corpus. It has been cited 9 times, with 9 citing works in its 1-hop citation network. Its calibrated FAIR score is 67/100.
Ranks in the top 44% 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.
“https://doi.org/10.7910/DVN/QBMC9D”
The data availability statement provides a DOI (10.7910/DVN/QBMC9D) for the study's own dataset, which is a persistent identifier scheme.
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 data availability statement names 'Harvard Dataverse', a repository listed in re3data/FAIRsharing, as the holder of 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
“The data that support the findings of this study, including all transcript assemblies and source code, are openly available in the Harvard Dataverse at https://doi.org/10.7910/DVN/QBMC9D”
The dataset's DOI appears only in the body text (data availability statement), 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 data that support the findings of this study, including all transcript assemblies and source code, are openly available in the Harvard Dataverse at https://doi.org/10.7910/DVN/QBMC9D”
The statement points to a repository record with a DOI, which is category 3 in the Colavizza classification. [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
“Altogether, 9,581 transcripts were identified in the merged assembly: 4,510 transcripts corresponding to annotated E. coli genes ( https://dataverse.harvard.edu/api/access/datafile/6562494 ) and 5,071 other transcripts ( https://dataverse.harvard.edu/api/access/datafile/6562495 )”
The dataset's content is described in running prose, not in a section, table, or enumerated list that itemises files or variables. [majority verdict 'partial' (4/5 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 data that support the findings of this study, including all transcript assemblies and source code, are openly available in the Harvard Dataverse at https://doi.org/10.7910/DVN/QBMC9D”
The data are stated to be openly available with no precondition such as embargo, registration, or application. [majority verdict 'yes' (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
“openly available”
The data availability statement explicitly labels the data as 'openly available', which is a recognized access-level label. [majority verdict 'yes' (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 does not involve human-subject or sensitive data, so no gatekeeper is named or required.
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 in the paper states how long the data will remain available or makes any persistence commitment. [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 paper does not specify the file format of the deposited data (e.g., GFF, CSV, TSV). [majority verdict 'no' (4/5 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
“Gene Ontology (GO)”
The paper uses the Gene Ontology, a community standard vocabulary, to classify gene roles. [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'
“assembly ASM584v2”
The paper provides an identifier for the reference genome (assembly ASM584v2) used to align and assemble the data.
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 stated in the paper; the only license mentioned is for the article itself (CC BY 4.0).
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 for the deposited dataset.
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'
“All source code is publicly available on GitHub at https://github.com/btjaden/Compendium.git”
A machine-resolvable URL to a code repository (GitHub) is given for the study's own 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)
“R15 GM102755”
The paper includes an award/grant number (R15 GM102755) attached to a named funder (National Institutes of Health).
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
“HISAT2 version 2.2.1”
The paper names specific tools and versions (e.g., HISAT2 2.2.1, StringTie 2.2.1) used to produce the data.
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, codebook, data dictionary) is named as accompanying the data, and no variable-definition table is provided for the study's own data. [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
0.345
From this paper's citation signal
Citation Network Contribution
0.0714
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 9 citers.
NIGMS NIH HHS
Grant: R15 GM102755
National Institutes of Health
Grant: 2R15GM102755-02A1
System and Methods for Analysis of Bacterial Transcriptomes
National Institutes of Health
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals
Escherichia coli transcriptome assembly from a compendium of RNA-seq data sets
Escherichia coli transcriptome assembly from a compendium of RNA-seq data sets