Ensembl 2025 is a dataset published in Nucleic Acids Research (2024). On theSindex it has a DataRank of 3.8, placing it in the top 6% of the data-sharing corpus. It has been cited 587 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 63/100.
Ranks in the top 6% 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.
“All Ensembl integrated data are available without restriction from the main website ( www.ensembl.org )”
The strongest identifier is a URL (web address), not a persistent identifier 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'
“All Ensembl integrated data are available without restriction from the main website ( www.ensembl.org )”
The holder is the Ensembl website, which is not a curated repository listed in re3data/FAIRsharing. [majority verdict 'partial' (2/5 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
“All Ensembl integrated data are available without restriction from the main website ( www.ensembl.org ), the component sites ( www.metazoa.ensembl.org , www.plants.ensembl.org , www.fungi.ensembl.org , www.protists.ensembl.org and www.bacteria.ensembl.org ), the Rapid Release site ( https://rapid.ensembl.org ) and Beta Ensembl ( beta.ensembl.org ), in bulk from the FTP site ( https://ftp.ensembl.org ) and programmatically via the REST API ( https://rest.ensembl.org ).”
The dataset identifier (URL) appears only in the body text, not as a reference-list entry. [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
“All Ensembl integrated data are available without restriction from the main website ( www.ensembl.org ), the component sites ( www.metazoa.ensembl.org , www.plants.ensembl.org , www.fungi.ensembl.org , www.protists.ensembl.org and www.bacteria.ensembl.org ), the Rapid Release site ( https://rapid.ensembl.org ) and Beta Ensembl ( beta.ensembl.org ), in bulk from the FTP site ( https://ftp.ensembl.org ) and programmatically via the REST API ( https://rest.ensembl.org ).”
The statement points to URLs rather than 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
“Ensembl is an open platform integrating publicly available genomics data across the tree of life with a focus on eukaryotic species related to human health, agriculture and biodiversity.”— not found in the paper; verdict downgraded
The dataset is described in running prose, not in an itemised inventory. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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 Ensembl integrated data are available without restriction from the main website ( www.ensembl.org )”
The paper states the data are available without restriction, 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
“available without restriction”
The paper explicitly labels the data as 'available without restriction' which is a natural-language equivalent of 'open access'. [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 paper does not mention that the data are sensitive or human-subject, 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
The paper states the data are available now but does not commit to a retention period or permanent archival; only availability timing is given. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 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'
“GFF3 annotation files”
The paper names open, community-standard formats. [majority verdict 'yes' (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
“MANE (v1.3 in Ensembl release 112) encompasses >99% of human protein-coding genes and contains 19 288 MANE Select transcripts”— not found in the paper; verdict downgraded
MANE is a community standard for transcript annotation, registered in FAIRsharing. [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'
No identifier for an external resource other than the paper's own dataset is given.
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 named license is attached to the data; the article's CC-BY license covers the paper only.
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'
“Ensembl release 112”
Version tokens for the data are given. [majority verdict 'yes' (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'
“Ensembl code is available from GitHub ( https://github.com/Ensembl ) under an open source Apache 2.0 licence.”
A machine-resolvable locator for the code is provided. [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)
“Wellcome Trust [222155/Z/20/Z, 226083/Z/22/Z, 226458/Z/22/Z]; National Human Genome Research Institute of the National Institutes of Health [U24HG007234, U41HG010972, U24HG002223, R01HG010485, U24HG011451, U24HG007497]”
Award/grant numbers are given for the funding. [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
“Prokka, InterProScan and AMRFinderPlus”— not found in the paper; verdict downgraded
The paper names specific tools and software used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper]
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) 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
0.957
From this paper's citation signal
Citation Network Contribution
2.8
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.
Wellcome Trust
Grant: 222155/Z/20/Z
Wellcome Trust
Grant: 226083/Z/22/Z
Wellcome Trust
Grant: 226458/Z/22/Z
Wellcome Trust
Grant: U24HG007234
Wellcome Trust
Grant: U41HG010972
Wellcome Trust
Grant: U24HG002223
Wellcome Trust
Grant: R01HG010485
Wellcome Trust
Grant: U24HG011451
Wellcome Trust
Grant: U24HG007497
Wellcome Trust
Grant: 75N93019C00077
Wellcome Trust
Grant: 1R01GM135247
Biotechnology and Biological Sciences Research Council
Grant: BB/W019108/1
Ensembl in a new era - deep genome annotation of domesticated animal species and breeds
Biotechnology and Biological Sciences Research Council
Grant: BB/T015608/1
BBSRC-NSF/BIO PanOryza: Globally coordinated genomes, proteomes and pathways for rice
Biotechnology and Biological Sciences Research Council
Grant: BB/X018695/1
Ensembl plant populations: integrating trait analyses and population-based sequence variants into a browsable genomic context
UK Medical Research Council
Grant: MR/S000453/1
WormBase: expanding the reference resource for helminth research
Horizon 2020
Grant: 825575
European Joint Programme on Rare Diseases
Horizon 2020
Grant: 817923
Advancing European Aquaculture by Genome Functional Annotation
Horizon 2020
Grant: 817998
The regulatory GENomE of SWine and CHicken: functional annotation during development
Horizon 2020
Grant: 815668
BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle
Gordon and Betty Moore Foundation
Grant: CBMF8897
NIGMS NIH HHS
Grant: R01 GM135247
NHGRI NIH HHS
Grant: U24 HG011853
NHGRI NIH HHS
Grant: U41 HG007234
National Institutes of Health
Grant: 5U24HG007497-07
Identifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human Genomes
National Institutes of Health
Grant: 5U41HG010972-02
The WashU-UCSC-EBI Human Genome Reference Center
National Institutes of Health
Grant: 5U24HG011451-03
Generating a full-length reference transcriptome for human protein-coding genes
Wellcome Trust
Grant: 226458
Darwin Tree of Life Extension Funding
National Institutes of Health
Grant: 5R01GM135247-02
Cross-species conservation of cell-type and single-cell specific isoform expression
National Institutes of Health
Grant: 5U24HG002223-20
WormBase: a core data resource for C. elegans and other nematodes
Wellcome Trust
Grant: 222155
Ensembl: A Comprehensive Reference Resource for Genomics
European Commission
Grant: 101059492
Biodiversity Genomics Europe
National Institutes of Health
Grant: 1R01HG010485-01A1
Enabling Comparative Pangenomics
European Commission
Grant: 101094718
A European infrastructure for farmed animal genotype to phenotype research
National Institutes of Health
Grant: 2U24HG007234-09
GENCODE: comprehensive reference genome annotation for human and mouse
Wellcome Trust
Grant: 226083
Primary Annotated Resources to Advance Discovery In Genomic Medicine (PARADIGM)
Horizon Europe programme
Wellcome Trust
FWCI
98.67
Citation Percentile
1.0%
Citation Trend
Fields of Study
MeSH Terms
Keywords