GENCODE: reference annotation for the human and mouse genomes in 2023 is a dataset published in Nucleic Acids Research (2022). On theSindex it has a DataRank of 5.1, placing it in the top 4.2% of the data-sharing corpus. It has been cited 663 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 54/100.
Ranks in the top 4% 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.
“Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.”
The paper provides a web address (URL) for the data, 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'
“Each release is versioned and made available immediately upon release from Ensembl and https//www.gencodegenes.org”
The holders named are Ensembl (a genome browser) and the GENCODE website (a project site), not a dedicated data repository. [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
“The current human release is GENCODE 41 (July 2022) and the current mouse release is GENCODE M30 (July 2022).”
The dataset version string appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (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
“No new data were generated or analysed in support of this research.”
The data-availability statement declares no new data were generated, so it does not point to a repository record. [majority verdict 'no' (4/5 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 1. Total numbers of genes and transcripts in the GENCODE 41 (human) and GENCODE M30 (mouse) releases by gene functional biotype.”
The paper includes a table (Table 1) that itemises the counts of genes and transcripts, serving as an itemised inventory of the dataset. [majority verdict 'yes' (4/5 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'
“We make all our annotation freely available to support genome interpretation and biomedical research.”
The paper states the data are freely available with no precondition.
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
“We make all our annotation freely available to support genome interpretation and biomedical research.”
The paper explicitly states the data are 'freely available', which is a direct access-level label.
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 describes no sensitive or human-subject data, so 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
“Each release is versioned and made available immediately upon release from Ensembl and https//www.gencodegenes.org”
The paper states the data are available immediately upon release but does not specify a retention period. [majority verdict 'partial' (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'
“Ensembl FTP site (ftp://ftp.ensembl.org/pub/), which includes genesets in GFF3, Genbank and GTF formats”— not found in the paper; verdict downgraded
The paper names GFF3, GTF, and Genbank formats, which are open, community-standard formats. [downgraded to 'partial' — no verifiable quote from the paper]
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, Dublin Core) is named for the data. [majority verdict 'no' (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'
No identifier (accession, DOI, RRID, etc.) for an external resource is provided in the text.
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'
The paper does not name any licence for the data itself; only the article's licence is mentioned.
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 current human release is GENCODE 41 (July 2022) and the current mouse release is GENCODE M30 (July 2022).”
The paper provides version tokens (GENCODE 41, M30) for the data snapshots.
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'
“we have implemented the use of the tmerge pipeline (https://github.com/julienlag/tmerge) within TAGENE”— not found in the paper; verdict downgraded
The paper gives a GitHub URL for the tool, which is a machine-resolvable locator for the study's code. [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)
“National Human Genome Research Institute of the National Institutes of Health [U41HG007234, R01HG004037]; Wellcome Trust [WT222155 /Z/20/Z]”
The paper includes specific grant numbers (U41HG007234, R01HG004037, WT222155/Z/20/Z) for the funding.
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 implemented the use of the tmerge pipeline (https://github.com/julienlag/tmerge) within TAGENE”— not found in the paper; verdict downgraded
The paper names specific tools and pipelines (e.g., tmerge, TAGENE) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [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
No documentation object (README, codebook) is named as travelling with the data. [majority verdict 'no' (2/5 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
0.975
From this paper's citation signal
Citation Network Contribution
4.1
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.
National Institutes of Health
Grant: U41HG007234
National Institutes of Health
Grant: R01HG004037
Wellcome Trust
Grant: WT222155/Z/20/Z
NHGRI NIH HHS
Grant: U24 HG007234
Biotechnology and Biological Sciences Research Council
Grant: BB/T01461X/1
National Institutes of Health
Grant: 1R01HG004037-01A1
Regulatory Morif Discovery in the Human Genome Using Comparative Genomics
Wellcome Trust
Grant: 222155
Ensembl: A Comprehensive Reference Resource for Genomics
National Institutes of Health
Grant: 5U41HG007234-08
GENCODE: comprehensive genome annotation for human and mouse
Wellcome Trust
European Molecular Biology Laboratory
FWCI
37.83
Citation Percentile
1.0%
Influential Citations
28
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals