The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals is a dataset published in Nucleic Acids Research (2020). On theSindex it has a DataRank of 4.2, placing it in the top 5.3% of the data-sharing corpus. It has been cited 204 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 50/100.
Ranks in the top 5% 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.
“Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/.”— not found in the paper; verdict downgraded
The paper gives a web address (URL) for the data, not a persistent identifier scheme. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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'
“Bgee, documentation, and links to resources used, are available at https://bgee.org/.”— not found in the paper; verdict downgraded
The data are held on the Bgee website, which is a non-repository host (not a curated archive like GEO or Zenodo). [downgraded to 'no' — no verifiable quote from the paper]
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
“Bgee, documentation, and links to resources used, are available at https://bgee.org/.”— not found in the paper; verdict downgraded
The dataset identifier (URL) appears only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper]
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-availability statement provides a link to the Bgee website but no accession or persistent identifier for a specific dataset record. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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
“Table 2. Data statistics for release Bgee 14.1 per species for the 29 species included in this version”
The paper provides an itemised inventory of the data in a table (Table 2) listing per-species statistics. [majority verdict 'yes' (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'
“All data are published under the Creative Commons Zero license (CC0).”
The data are stated to be published under CC0, implying unconditional open access with no precondition. [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
“All data are published under the Creative Commons Zero license (CC0).”
The paper licenses the data under CC0, which is a waiver of all rights and implies open access, but it does not explicitly label the access level with a standard vocabulary term like 'open access'. [majority verdict 'partial' (3/5 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 are published under the Creative Commons Zero license (CC0).”
The Bgee data are not sensitive and are released openly under CC0; 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 release 14.1 includes 29 animal species, and is available at https://bgee.org/.”— not found in the paper; verdict downgraded
The paper states the data are available now but does not mention how long they will persist. [downgraded to 'no' — no verifiable quote from the paper] [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'
“We provide TSV files to retrieve, for each species: (i) annotated and processed expression values for RNA-Seq and Affymetrix data and (ii) calls of presence/absence of expression with confidence and rank scores generated from all data types.”— not found in the paper; verdict downgraded
The paper names TSV, an open, non-proprietary file format. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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
“To describe the anatomy of diverse animals, we use the Uberon ontology (17).”— not found in the paper; verdict downgraded
The paper names the Uberon ontology, a community standard for anatomy, and also uses Gene Ontology and NCBI Taxonomy. [downgraded to 'partial' — no verifiable quote from the paper]
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'
“We have curated the GTEx human dataset phs000424.v6.p1 (7).”
The paper gives a dbGaP accession (phs000424.v6.p1) for an external resource (GTEx) that the data depend on. [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'
“All data are published under the Creative Commons Zero license (CC0).”
The paper attaches an open standard license (CC0) to the data. [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 release 14.1 includes 29 animal species”
The paper gives a version token 'release 14.1' for the data. [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'
“Source code and annotations are available in the GitHub repository (https://github.com/BgeeDB).”— not found in the paper; verdict downgraded
The paper provides a machine-resolvable URL to a code repository (GitHub) for the study's own code. [downgraded to 'partial' — no verifiable quote from the paper]
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)
“Swiss National Science Foundation [31003A 173048, 31003A 153341, 31003A133011, CRSII3160723]; SystemsX project AgingX, PNR [407540167149 (BioSODA)]; NIH Award [U01CA215010 (OncoMX)]; European Union’s Horizon 2020 research and innovation program [863410].”
The paper gives specific award numbers for multiple 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
“We use Kallisto (41) to generate pseudo-counts per transcript”
The paper names specific tools (Kallisto, IQRray, gcRMA) used to produce 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
“We provide TSV files to retrieve, for each species: (i) annotated and processed expression values for RNA-Seq and Affymetrix data and (ii) calls of presence/absence of expression with confidence and rank scores generated from all data types.”— not found in the paper; verdict downgraded
Variable definitions are described in the article text and tables, but no separate documentation object is named as travelling with the data. [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
0.798
From this paper's citation signal
Citation Network Contribution
3.4
From 100 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 100 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: 407540_167149
NIH
Grant: U01CA215010
Horizon 2020
Grant: 863410
INODE - Intelligent Open Data Exploration
Swiss National Science Foundation
Grant: 173048
The evolution of function in organs and genes in light of expression patterns
Swiss National Science Foundation
Grant: 153341
Bioinformatics search for adaptive evolution in vertebrate development
Swiss National Science Foundation
Grant: 133011
Bioinformatic study of molecular evolution in the context of animal development and anatomy
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: 160723
Genome evolution under sexual and asexual reproduction
Swiss National Science Foundation
Grant: 167149
Bio-SODA: Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data
Swiss Institute of Bioinformatics
Canton de Vaud
Fields of Study
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