Ensembl 2024 is a dataset published in Nucleic Acids Research (2023). On theSindex it has a DataRank of 5.9, placing it in the top 3.4% of the data-sharing corpus. It has been cited 747 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 19/100.
Ranks in the top 3% 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 paper provides URLs to the data but no persistent identifier string (DOI, Handle, ARK, or repository accession) for the dataset itself. [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'
“Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades.”— not found in the paper; verdict downgraded
The data are held by Ensembl, which is a named host but not a repository in the curated archive sense. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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
No dataset identifier appears anywhere in the paper, either in the reference list or body text. [majority verdict 'no' (4/5 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 (https://www.ensembl.org), the Rapid Release site (https://rapid.ensembl.org), in bulk from the FTP site (https://ftp.ensembl.org) and programmatically via the REST API (https://rest.ensembl.org).”— not found in the paper; verdict downgraded
The statement points to a repository (Ensembl) but does not provide an accession, DOI, or persistent link to a specific record, so it is category 2/partial. [downgraded to 'no' — no verifiable quote from the paper] [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
“Ensembl now offers annotation of promoters and open chromatin regions across different cell types and developmental time points for Pig, Chicken, Atlantic salmon, Turbot and European seabass in collaboration with the GENE-SWitCH and AQUA-FAANG consortia (Figure 2).”— not found in the paper; verdict downgraded
The paper describes the data content in running prose rather than an itemized inventory (section, table, or list). [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'
“Ensembl data, software, and tools are freely available.”— not found in the paper; verdict downgraded
The text states that the data are freely available with no stated precondition. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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
“Ensembl data, software, and tools are freely available.”— not found in the paper; verdict downgraded
The paper explicitly uses the label 'freely available' for the data, which is a natural-language equivalent of the access rights vocabulary. [downgraded to 'partial' — no verifiable quote from the paper] [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 Ensembl integrated data are available without restriction from the main website (https://www.ensembl.org), the Rapid Release site (https://rapid.ensembl.org), in bulk from the FTP site (https://ftp.ensembl.org) and programmatically via the REST API (https://rest.ensembl.org).”— not found in the paper; verdict downgraded
The paper states that all data are available without restriction, indicating no sensitive data requiring a gatekeeper is present.
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
“Ensembl is recognised as a Global Core BioData Resource and ELIXIR Core Data Resource highlighting the fundamental role it plays in life sciences research for long-term preservation and open access to high-quality annotated genomic data.”— not found in the paper; verdict downgraded
The paper claims 'long-term preservation', which is a persistence commitment for the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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'
No file format for the released data is named in the text; the mention of GFF3 in future directions does not apply to the current data. [majority verdict 'no' (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
“We have implemented the GA4GH Beacon v2 specification to enable the retrieval of rich variant annotations and enable the improved interoperability of our data.”— not found in the paper; verdict downgraded
The paper names GA4GH Beacon v2, a community standard for data exchange, applied to the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 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 update of the human genome assembly to GRCh38.p14 allowed us to manually annotate additional 'patch' regions”
The paper provides the assembly build ID 'GRCh38.p14' for a resource (the human genome assembly) that the data builds upon.
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; the CC BY license applies to the article, not the data.
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 latest farmed animal datasets have been made available via the Rapid Release site and will be included on the next main Ensembl site in release, 111.”
The paper names a version token ('release 111') 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'
“Ensembl code is available from GitHub (https://github.com/Ensembl) under an open source Apache 2.0 licence.”— not found in the paper; verdict downgraded
The paper provides a machine-resolvable locator (GitHub URL) 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)
“Wellcome Trust [222155/Z/20/Z]”— not found in the paper; verdict downgraded
An award number is provided for a named funder. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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
“We have continued to generate annotations for assemblies from global biodiversity initiatives, such as the Darwin Tree of Life project”
The paper describes the production of data in generic terms without naming specific instruments, kits, or software versions. [majority verdict 'partial' (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
“A documented overview of our different genome annotation methodologies is available at https://rapid.ensembl.org/info/genome/genebuild/index.html, with the type of annotation produced indicated on each species’ home page.”— not found in the paper; verdict downgraded
The paper describes a documentation object (a documented overview) but it is not shipped with the data; the paper itself contains only running prose descriptions. [downgraded to 'no' — no verifiable quote from the paper]
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
0.993
From this paper's citation signal
Citation Network Contribution
4.9
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
National Human Genome Research Institute of the National Institutes of Health
Grant: U24HG007234
National Human Genome Research Institute of the National Institutes of Health
Grant: U41HG010972
National Human Genome Research Institute of the National Institutes of Health
Grant: U24 HG002223,
National Human Genome Research Institute of the National Institutes of Health
Grant: R01HG010485
National Human Genome Research Institute of the National Institutes of Health
Grant: U24HG011451
National Human Genome Research Institute of the National Institutes of Health
Grant: U24HG007497
National Institute of Allergy and Infectious Diseases of the National Institutes of Health
Grant: 75N93019C00077
The Biotechnology and Biological Sciences Research Council
Grant: BB/W019108/1
Ensembl in a new era - deep genome annotation of domesticated animal species and breeds
The Biotechnology and Biological Sciences Research Council
Grant: BB/T015608/1
BBSRC-NSF/BIO PanOryza: Globally coordinated genomes, proteomes and pathways for rice
The Biotechnology and Biological Sciences Research Council
Grant: BB/P016855/1
The Biotechnology and Biological Sciences Research Council
Grant: BB/S02011X/1
A FAIR community resource for pathogen, host, interactions to enhance global food security and human health
The Biotechnology and Biological Sciences Research Council
Grant: BB/T01461X/1
BBSRC-NSF/BIO: Next generation collaborative annotation of genomes and synteny
The Biotechnology and Biological Sciences Research Council
Grant: BB/W002965/1
2020BBSRC-NSF/BIO: REDEFINE - Development of efficient, large-scale metagenomics sequence comparison algorithms to facilitate novel genomic insights
UK Medical Research Council
Grant: MR/S000453/1
WormBase: expanding the reference resource for helminth research
Wellcome Trust
Grant: 226458/Z/22/Z
Wellcome Trust
Grant: WT212925/Z/18/Z
Wellcome Trust
Grant: 226083/Z/22/Z
European Union's Horizon 2020
Grant: 731060 (INFRAVEC2)
European Union's Horizon 2020
Grant: 733161 (MultipleMS)
European Union's Horizon 2020
Grant: 825575
European Joint Programme on Rare Diseases
European Union's Horizon 2020
Grant: 817923 (AQUA-FAANG)
European Union's Horizon 2020
Grant: 817998 (GENE-SWitCH)
European Union's Horizon 2020
Grant: 815668 (BovReg)
Horizon Europe programme
Grant: 101059492
Biodiversity Genomics Europe
Horizon Europe programme
Grant: 101094718
A European infrastructure for farmed animal genotype to phenotype research
Gordon and Betty Moore Foundation
Grant: CBMF8897
NHGRI NIH HHS
Grant: U41 HG007234
NHGRI NIH HHS
Grant: U24 HG002223
European Commission
Grant: 817923
Advancing European Aquaculture by Genome Functional Annotation
National Institutes of Health
Grant: 3U41HG002223-17S1
WormBase: a core data resource for C. elegans and other nematodes
Wellcome Trust
Grant: 226458
Darwin Tree of Life Extension Funding
European Commission
Grant: 731060
Research Infrastructures for the control of vector-borne diseases
Wellcome Trust
Grant: 222155
Ensembl: A Comprehensive Reference Resource for Genomics
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: 5U24HG002223-20
WormBase: a core data resource for C. elegans and other nematodes
European Commission
Grant: 815668
BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle
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
National Institutes of Health
Grant: 1R01HG010485-01A1
Enabling Comparative Pangenomics
European Commission
Grant: 733161
Multiple manifestations of genetic and non-genetic factors in Multiple Sclerosis disentangled with a multi-omics approach to accelerate personalised medicine
National Institutes of Health
Grant: 2U24HG007234-09
GENCODE: comprehensive reference genome annotation for human and mouse
Wellcome Trust
Grant: 212925
INVAR – assigning function to orphan amino-acid variants
European Commission
Grant: 817998
The regulatory GENomE of SWine and CHicken: functional annotation during development
Wellcome Trust
Grant: 226083
Primary Annotated Resources to Advance Discovery In Genomic Medicine (PARADIGM)
European Molecular Biology Laboratory
Wellcome Trust
ELIXIR
Open Targets
Fields of Study
MeSH Terms
Keywords
Additional file 2 of MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization
Additional file 2 of MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization
Additional file 3 of MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization
Additional file 3 of MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization
Additional file 1 of MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization
Additional file 1 of MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization