Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis is a dataset published in PeerJ (2023). On theSindex it has a DataRank of 0.165, placing it in the top 70.2% of the data-sharing corpus. It has been cited 2 times, with 1 citing works in its 1-hop citation network. Its calibrated FAIR score is 50/100.
Ranks in the top 70% 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 resource is available from: https://maayanlab.github.io/dex-benchmark”
The paper provides a web URL for the resource, not a persistent identifier in a recognised PID scheme. [majority verdict 'partial' (4/5 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 Dex-Benchmark resource is available as a web interface hosted on GitHub pages at https://maayanlab.github.io/dex-benchmark”
The data are hosted on a GitHub Pages website, which is not a curated data repository. [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 resource is available from: https://maayanlab.github.io/dex-benchmark”
The dataset identifier (URL) appears only in the body text, not in the reference list.
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 following information was supplied regarding data availability: The code is available at GitHub and Zenodo: - https://github.com/MaayanLab/dex-benchmark . - Xie, Zhuorui. (2023). Source code and file for a publication titled: "Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis" (10-11-2023). Zenodo. https://doi.org/10.5281/zenodo.8433206 .”
The formal data-availability statement only points to the code repository, not to the dataset itself; the dataset's location is given in the body text as a URL. [majority verdict 'no' (2/5 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
“The resource provides access to a collection of curated RNA-seq, L1000, and ChIP-seq data from dexamethasone treatment as well as genetic perturbations of its known targets.”
The dataset content is described in running prose, not in an itemised inventory.
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 resource is available from: https://maayanlab.github.io/dex-benchmark”
The paper gives a public URL 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
“The resource is available from: https://maayanlab.github.io/dex-benchmark”
The paper describes the access action (the URL) but does not label the access level with a standard vocabulary term. [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 data are not sensitive or human-subject; no gatekeeper is mentioned.
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 how long the data will be available or persistence commitment. [majority verdict 'no' (3/5 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 name the file format of the released datasets.
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, FAIRsharing) 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'
“GSE159094”
The paper includes a GEO accession for a source dataset used in the analysis.
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 reuse terms are stated for the dataset.
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 paper does not provide a version token or date for the released dataset. [majority verdict 'no' (4/5 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 code is available at GitHub and Zenodo: - https://github.com/MaayanLab/dex-benchmark . - Xie, Zhuorui. (2023). Source code and file for a publication titled: “Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis” (10-11-2023). Zenodo. https://doi.org/10.5281/zenodo.8433206 .”
The paper provides a machine-resolvable locator (GitHub URL and Zenodo DOI) for the study's 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)
“This work was funded by the National Institutes of Health (NIH) grants numbers OT2OD030160, U24CA224260, U24CA264250, U24CA271114, R01DK131525, and RC2DK131995.”
Award/grant numbers are attached to the named funder (NIH).
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
“L1000 Level 5 MODZ signatures for dexamethasone were queried and downloaded from the CLUE.io ( https://clue.io ) command app”
The paper names specific tools and data sources used to produce the compiled dataset. [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
No README, codebook, or data dictionary is mentioned as accompanying the data.
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
0.165
From this paper's citation signal
Citation Network Contribution
0
From 0 citing papers with measurable signal
This paper's DataRank is currently driven only by its base citation score. None of the citing papers had measurable citation signal.
Learn more about DataRank methodology →NIDDK NIH HHS
Grant: R01 DK131525
NIH HHS
Grant: OT2 OD036435
National Institutes of Health
Grant: OT2OD030160, U24CA224260, U24CA264250, U24CA271114, R01DK131525, and RC2DK131995
NCI NIH HHS
Grant: U24 CA264250
NCI NIH HHS
Grant: U24 CA271114
NCI NIH HHS
Grant: U24 CA224260
NIDDK NIH HHS
Grant: RC2 DK131995
NIH HHS
Grant: OT2 OD030160
FWCI
0.27
Citation Percentile
0.6%
Citation Trend
Fields of Study
MeSH Terms
Keywords