Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis is a dataset published in Nucleic Acids Research (2023). On theSindex it has a DataRank of 0.501, placing it in the top 38.3% of the data-sharing corpus. It has been cited 12 times, with 9 citing works in its 1-hop citation network. Its calibrated FAIR score is 54/100.
Ranks in the top 38% 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.
“full downloads of Plant Reactome data are available at https://plantreactome.gramene.org/download/currrent”
The only identifier is a URL, not a persistent identifier scheme (DOI, Handle, etc.).
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'
“The data and resources discussed above are available from the Download page, accessible from the main navigation bar at https://plantreactome.gramene.org”
The holder is the Plant Reactome project website, not a curated repository listed in re3data.
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 data and resources discussed above are available from the Download page, accessible from the main navigation bar at https://plantreactome.gramene.org”
The dataset's identifier appears only in body text, not in the reference list.
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 and resources discussed above are available from the Download page, accessible from the main navigation bar at https://plantreactome.gramene.org”
The statement points to a URL on the project's own site, not a repository record. [majority verdict 'partial' (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
“the Plant Reactome hosts 2129 gene products mapped to 1953 reactions associated with 339 manually curated reference rice pathways and pathway projections for 129 other photoautotrophic species”
The dataset content is described in running prose, not in a dedicated section, table, or list. [majority verdict 'partial' (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'
“Plant Reactome ( https://plantreactome.gramene.org ) is a freely accessible, comprehensive plant pathway knowledgebase.”
The paper states the data are freely accessible 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
“Plant Reactome is a freely accessible, comprehensive plant pathway knowledgebase.”— not found in the paper; verdict downgraded
The paper explicitly labels the data as 'freely accessible', a natural-language synonym for open access, satisfying the access-level label requirement. [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
The data are not sensitive and no gatekeeper is mentioned.
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
“In the current Gramene release #67, August 2023, the Plant Reactome hosts 2129 gene products mapped to 1953 reactions associated with 339 manually curated reference rice pathways”
The paper states the data are available now (current release) but gives no persistence commitment, only timing. [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'
“Images of all pathways and reactions are also available in PNG and SVG formats.”
PNG and SVG are open, non-proprietary 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
“Plant Reactome biocurators utilize Gene Ontology (GO) ( 14 ) and Plant Ontology (PO) ( 15 ) to describe the gene function(s) and their relationships with plant growth and development.”— not found in the paper; verdict downgraded
GO and PO are community standards registered in FAIRsharing. [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'
“Using the publicly available gene expression data ( 61 ) from Expression Atlas (E-GEOD-67588), we found this gene expresses”
The paper includes a GEO accession (E-GEOD-67588) for a resource other than its 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 for the data is stated; the CC BY 4.0 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'
“Gramene release #67, August 2023”
The paper provides a version token (release #67 and version 23) for the data snapshot. [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'
No code repository URL or DOI for the study's own code is provided.
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)
“S.N. acknowledges funding from the National Aeronautics and Space Administration (NASA), USA [80NSSC22K0891]; P.J. acknowledges funding from NASA [#80NSSC22K0855], National Science Foundation, USA [2029854]”
Award numbers are given for the funding sources. [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 manually curate rice pathways based on information gathered from published experimental studies, functional annotations provided by GO and PO, and additional bioinformatic analysis”
The production method is described 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
“The file gk_current.sql.gz is a compressed dump of the MySQL database, while reactome.graphdb.gz is a compressed dump of the Neo4J database. Other files include text files describing mappings for ChEBI, NCBI, UniProt, Ensembl and miRBase to Plant Reactome pathways and reactions. Images of all pathways and reactions are also available in PNG and SVG formats.”
The variable/file definitions are described inside the article, not in a separate documentation object shipped with the data. [majority verdict 'partial' (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
0.385
From this paper's citation signal
Citation Network Contribution
0.116
From 8 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 9 citers.
National Aeronautics and Space Administration
Grant: 80NSSC22K0891
National Aeronautics and Space Administration
Grant: #80NSSC22K0855
National Science Foundation
Grant: 2029854
CIBR:BBSRC: PanOryza: Globally coordinated genomes, proteomes and pathways for rice
NIH
Grant: U24 HG012198
National Institutes of Health
Grant: 3U24HG012198-04S1
Reactome: An Open Knowledgebase of Human Pathways.
USDA-ARS
FWCI
1.12
Citation Percentile
0.8%
Citation Trend
Fields of Study
MeSH Terms
Keywords