The PanOryza pangene catalog of Asian cultivated rice is a dataset published in Genome Research (2025). On theSindex it has a DataRank of 0.104, placing it in the top 77.8% of the data-sharing corpus. It has been cited 1 time, with 1 citing works in its 1-hop citation network. Its calibrated FAIR score is 54/100.
Ranks in the top 78% 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.
“A permanent DOI has also been created for the pangene matrix and identifiers (https://zenodo.org/records/14772953)”— not found in the paper; verdict downgraded
The paper asserts a DOI for the dataset, and the given URL resolves to a Zenodo record, which is a persistent identifier. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 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'
“Zenodo”
The paper names Zenodo, a repository listed in re3data/FAIRsharing, as the holder of the data. [majority verdict 'yes' (3/5 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
“Data access The input data for running GET_PANGENES pipeline and the output files generated by the pipeline have been deposited at Zenodo (https://zenodo.org/records/14772953).”— not found in the paper; verdict downgraded
The dataset identifier appears only in the body text, not in a reference list entry. [downgraded to 'no' — no verifiable quote from the paper] [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
“Data access The input data for running GET_PANGENES pipeline and the output files generated by the pipeline have been deposited at Zenodo (https://zenodo.org/records/14772953).”— not found in the paper; verdict downgraded
The statement points to a repository record with a link (Colavizza category 3). [downgraded to 'partial' — no verifiable quote from the paper] [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
“We identify 25,178 core pangenes shared across all cultivars, alongside cultivar-specific and family-enriched genes.”
The dataset's content is described in running prose rather than an itemised inventory. [majority verdict 'partial' (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'
“The input data for running GET_PANGENES pipeline and the output files generated by the pipeline have been deposited at Zenodo (https://zenodo.org/records/14772953).”— not found in the paper; verdict downgraded
The data are deposited in a public repository 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
“The input data for running GET_PANGENES pipeline and the output files generated by the pipeline have been deposited at Zenodo (https://zenodo.org/records/14772953).”— not found in the paper; verdict downgraded
The paper describes the deposit action but does not apply an explicit access-level label such as 'open access'. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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
The data are not 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
No statement about how long data will persist or when they become available beyond the current deposit. [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'
“We first collected whole-genome sequences, gene and protein sequences (all FASTA format), and gene model coordinates (GFF format) for the RPRP rice population.”
FASTA and GFF are open, community-standard formats named for the data. [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
No community-standard vocabulary or checklist is explicitly named for the dataset itself. [majority verdict 'no' (2/5 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'
“AlphaFold models for O. sativa (reference id: UP000059680) were retrieved from the AlphaFold protein structure database”
The paper includes an identifier (UniProt proteome ID) for a resource used in the analysis, not the own dataset. [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'
No license is stated for the data; the article's CC-BY license does not apply to 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'
No version token or date is provided for the dataset snapshot. [majority verdict 'no' (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'
“Code is available at GitHub (GET_PANGENES: https://github.com/Ensembl/plant-scripts/blob/master/pangenes/ ; Nipponbare merged genes: https://github.com/Ensembl/plant-scripts/tree/master/scripts ).”
Machine-resolvable code forge URLs are provided. [majority verdict 'yes' (3/5 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)
“Financial support was provided by the Biotechnology and Biological Sciences Research Council (BB/T015691/1 and BB/T015608/1)”
The paper includes award numbers 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 ran the GET_PANGENES pipeline (version 11012024) (Contreras-Moreira et al. 2023), which performs WGA using minimap2 (version 2.17) (Li 2018), followed by BEDTools intersect (Quinlan and Hall 2010) to determine overlaps in each pairwise alignment.”— not found in the paper; verdict downgraded
Specific tools with version numbers are named for data production. [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
“Supplemental Table S1 contains the matrix of pangenes, with their stable identifier (column 1) and then 16 further columns, one per input genome, containing transcript identifiers (if any) from each genome that have been mapped to that pangene.”
The variable definitions are provided inside the article (Supplemental Table S1), not as a separate file shipped with 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
0.104
From this paper's citation signal
Citation Network Contribution
0
From 0 citing papers with measurable signal
This paper's DataRank is currently driven only by its base citation score. None of the citing papers had measurable citation signal.
Learn more about DataRank methodology →Biotechnology and Biological Sciences Research Council
Grant: BB/T015691/1
BBSRC-NSF/BIO PanOryza: Globally coordinated genomes, proteomes and pathways for rice
Biotechnology and Biological Sciences Research Council
Grant: BB/T015608/1
BBSRC-NSF/BIO PanOryza: Globally coordinated genomes, proteomes and pathways for rice
the U.S. National Science Foundation's Directorate for Biological Sciences
Grant: 2029854
CIBR:BBSRC: PanOryza: Globally coordinated genomes, proteomes and pathways for rice
the U.S. National Science Foundation's Directorate for Biological Sciences
Grant: IOS-1922871
United States Department of Agriculture's Agriculture Research Service
Grant: USDA ARS 8062-21000-051-00D
CSIC
Grant: FAS2022_052
Government of Aragón
Grant: A08_23R
U.S. National Institutes of Health
Grant: R01 GM087221
Wellcome Trust
Grant: 222155/Z/20/Z
Wellcome Trust
Wellcome Trust
Fields of Study
MeSH Terms
Keywords