Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools is a dataset published in Nucleic Acids Research (2024). On theSindex it has a DataRank of 0.868, placing it in the top 23.2% of the data-sharing corpus. It has been cited 33 times, with 29 citing works in its 1-hop citation network. Its calibrated FAIR score is 54/100.
Ranks in the top 23% 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.
No persistent identifier (DOI, Handle, ARK, or repository accession) is given 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'
“Bgee is a database to retrieve and compare gene expression patterns in multiple animal species.”— not found in the paper; verdict downgraded
Bgee is a named database website, not a repository from the class 1 list, so it is a non-repository host. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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 Bgee dataset itself does not have a persistent identifier and is not cited in the reference list. [majority verdict 'no' (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
“All data provided by Bgee are under the permissive license CC0.”
The statement points to the Bgee database itself, not to a repository record with an accession or DOI. [majority verdict 'partial' (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
The paper describes the dataset in running prose without an itemised inventory of files or variables. [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'
“All data provided by Bgee are under the permissive license CC0.”
The paper states the data are under CC0 and accessible via the Bgee website with no precondition. [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
“All data provided by Bgee are under the permissive license CC0.”
The paper mentions the license CC0 but does not use an explicit access-level label from the standard vocabulary. [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
“All data provided by Bgee are under the permissive license CC0.”
The data are open access and 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
“Bgee provides archived version with permanent URLs up to the 2016 release.”
The paper states that archived versions have permanent URLs, indicating persistence. [majority verdict 'yes' (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'
“TSV files containing information about experiment and libraries; TSV files containing read count information per cell population; and H5AD files containing read count information per cell.”
TSV and H5AD are open, community-standard formats. [majority verdict 'yes' (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
The paper uses standard ontologies such as Uberon, CL, and FBbt for annotating the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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'
The paper provides identifiers for external resources, such as experiment accessions ERP129698 and SRP222001. [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'
“CC0”
The paper states the data are under the open license CC0. [majority verdict 'yes' (4/5 passes agreed)]
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'
“Bgee version 15.2”
A version token 'Bgee 15.2' is given to identify the snapshot. [majority verdict 'yes' (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'
“https://github.com/BgeeDB/bgee_apps/”— not found in the paper; verdict downgraded
The paper provides a GitHub URL and Figshare DOIs for the code, which are machine-resolvable locators. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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)
“31003A_173048”
The paper lists grant numbers from funders. [majority verdict 'yes' (3/5 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
The paper names specific tools and packages used to produce the data, such as BgeeCall and BgeeDB. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 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
The paper describes the file formats and data structure in text, but does not include a separate documentation file or a table defining variables. [downgraded to 'no' — no verifiable quote from the paper] [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 →
Base Score Contribution
0.529
From this paper's citation signal
Citation Network Contribution
0.340
From 14 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 29 citers.
Swiss National Science Foundation
Grant: 31003A_173048
Swiss National Science Foundation
Grant: 31003A_153341
Swiss National Science Foundation
Grant: 31003A_133011
Swiss National Science Foundation
Grant: CRSII3_160723
Swiss National Science Foundation
Grant: 31003A_207853
Swiss National Science Foundation
Grant: PNR 407540_167149
NIH
Grant: U01CA215010
Horizon 2020 - Research and Innovation Framework Programme
Grant: 863410
INODE - Intelligent Open Data Exploration
Swiss National Science Foundation
Grant: 133011
Bioinformatic study of molecular evolution in the context of animal development and anatomy
Swiss National Science Foundation
Grant: 207853
Selection on gene expression at different time scales and vertebrate Evo-Devo
National Institutes of Health
Grant: 5U01CA215010-02
Integration of comprehensive cancer mutation and expression-associated data for biomarker evaluation and discovery
Swiss National Science Foundation
Grant: 173048
The evolution of function in organs and genes in light of expression patterns
Swiss National Science Foundation
Grant: 160723
Genome evolution under sexual and asexual reproduction
Swiss National Science Foundation
Grant: 153341
Bioinformatics search for adaptive evolution in vertebrate development
Swiss National Science Foundation
Grant: 167149
Bio-SODA: Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data
University of Lausanne
Service de la Santé Publique, Canton de Vaud
swissuniversities Programme Open Science
SIB Swiss Institute of Bioinformatics
FWCI
5.50
Citation Percentile
1.0%
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals