The Reactome Pathway Knowledgebase 2024 is a dataset published in Nucleic Acids Research (2023). On theSindex it has a DataRank of 4.5, placing it in the top 4.9% of the data-sharing corpus. It has been cited 1,383 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 75/100.
Ranks in the top 5% 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.
“Reactome Data 86: 10.5281/zenodo.10018440 (Data dump of version 86, both Neo4j and MySQL database)”
The paper provides a DOI for its own dataset (Zenodo), which is a persistent identifier scheme. [majority verdict 'yes' (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'
“We have created Zenodo packages for the versions of our software and data discussed in the article”
Zenodo is a named data repository, and the data are deposited there. [majority verdict 'yes' (4/5 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
“Reactome Data 86: 10.5281/zenodo.10018440 (Data dump of version 86, both Neo4j and MySQL database)”
The dataset identifier appears only in the body text (Data availability section), not as a reference-list entry.
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
“We have created Zenodo packages for the versions of our software and data discussed in the article: … Reactome Data 86: 10.5281/zenodo.10018440 (Data dump of version 86, both Neo4j and MySQL database)”— not found in the paper; verdict downgraded
The statement points to a repository record with a persistent identifier (Zenodo DOI). [downgraded to 'partial' — no verifiable quote from the paper] [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
“Table 1. Reactome content, version 78 (9/2021) versus 86 (9/2023)”
The paper includes an itemised inventory (Table 1) listing the dataset's content types and counts.
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 Reactome data are available in various formats from our downloads page ( https://reactome.org/download-data ).”
The text gives a direct download route with no stated 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
“Reactome is open-source and open-access.”
The paper explicitly labels the data as open-access in the Data availability section.
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 human-subject data; 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
“All Reactome data are available in various formats from our downloads page ( https://reactome.org/download-data ).”
Only availability timing (now) is stated; no persistence commitment is given. [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'
“Data dump of version 86, both Neo4j and MySQL database”
The paper names Neo4j and MySQL database formats for the data dump, which are not in the open/community-standard list (CSV, JSON, etc.). [majority verdict 'partial' (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
“Processes are systematically described in molecular detail to generate an ordered network of molecular transformations, resulting in an extended version of a classic metabolic map ( 4 ) generally compliant with the SBGN process description standard ( 5 ).”
The paper names multiple community standards (SBGN, Gene Ontology, ChEBI, RHEA, etc.) applied to the data.
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 11148 protein gene products now annotated in Reactome are 56.2% of the 19 831 protein-coding genes predicted in the current (GRCh38.p14) human genome assembly”
The paper gives the assembly identifier GRCh38.p14 for an external resource (the human genome assembly). [majority verdict 'yes' (3/5 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 specific license is named for the data; the CC-BY license applies to the article, not the dataset.
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'
“Reactome (version 86—September 2023)”
The paper gives a version token (version 86) for the data.
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'
“All software is available from our GitHub repositories ( https://github.com/reactome and https://github.com/reactome-pwp ), under terms that allow for free reuse and redistribution.”
The paper gives a machine-resolvable locator (GitHub URLs) for the study's own code. [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)
“The development of Reactome is supported by grants from the National Institutes of Health [U41HG003751, U24HG012198, U24HG011851, U54GM114833, U01CA239069]”
The paper provides specific grant numbers (award identifiers) 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
“The Reactome Knowledgebase, … provides manually curated molecular details of a broad range of normal and disease-related biological processes.”— not found in the paper; verdict downgraded
The production method is described generically (manual curation) without naming specific instruments or software versions. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 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
“Table 1. Reactome content, version 78 (9/2021) versus 86 (9/2023)”
The paper includes a table inside the article that defines the dataset's content, but no separate documentation object is named to accompany the data. [majority verdict 'partial' (3/5 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
1.1
From this paper's citation signal
Citation Network Contribution
3.4
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: U41HG003751
National Institutes of Health
Grant: U24HG012198
National Institutes of Health
Grant: U24HG011851
National Institutes of Health
Grant: U54GM114833
National Institutes of Health
Grant: U01CA239069
National Institutes of Health
Grant: 3U01CA239069-02S1
Reactome IDG portal: Pathway-based analysis and visualization of understudied human proteins
National Institutes of Health
Grant: 3U24HG012198-04S1
Reactome: An Open Knowledgebase of Human Pathways.
National Institutes of Health
Grant: 5U41HG003751-07
Reactome: An Open Knowledgebase of Human Pathways
National Institutes of Health
Grant: 5U24HG011851-03
Reactome and the Gene Ontology: Digital pathway convergence for core data resources
National Institutes of Health
Grant: 5U54GM114833-02
TRAINING
European Bioinformatics Institute
University of Toronto
Fields of Study
MeSH Terms
Keywords
Additional file 1 of Epigenetic scores of blood-based proteins as biomarkers of general cognitive function and brain health
Additional file 1 of Epigenetic scores of blood-based proteins as biomarkers of general cognitive function and brain health
Additional file 2 of Epigenetic scores of blood-based proteins as biomarkers of general cognitive function and brain health
Additional file 2 of Epigenetic scores of blood-based proteins as biomarkers of general cognitive function and brain health
Additional file 1 of A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
Additional file 1 of A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
Additional file 1 of Sodium-glucose cotransporter 2 inhibitors induce anti-inflammatory and anti-ferroptotic shift in epicardial adipose tissue of subjects with severe heart failure
Additional file 2 of Sodium-glucose cotransporter 2 inhibitors induce anti-inflammatory and anti-ferroptotic shift in epicardial adipose tissue of subjects with severe heart failure
Additional file 1 of Sodium-glucose cotransporter 2 inhibitors induce anti-inflammatory and anti-ferroptotic shift in epicardial adipose tissue of subjects with severe heart failure
Additional file 3 of Sodium-glucose cotransporter 2 inhibitors induce anti-inflammatory and anti-ferroptotic shift in epicardial adipose tissue of subjects with severe heart failure
Additional file 2 of Sodium-glucose cotransporter 2 inhibitors induce anti-inflammatory and anti-ferroptotic shift in epicardial adipose tissue of subjects with severe heart failure
Additional file 3 of Sodium-glucose cotransporter 2 inhibitors induce anti-inflammatory and anti-ferroptotic shift in epicardial adipose tissue of subjects with severe heart failure
Additional file 3 of Epigenetic scores of blood-based proteins as biomarkers of general cognitive function and brain health
Additional file 3 of Epigenetic scores of blood-based proteins as biomarkers of general cognitive function and brain health
Additional file 12 of A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
Additional file 11 of A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
Additional file 12 of A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
Additional file 4 of A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
Additional file 6 of A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
Additional file 11 of A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques