Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources is a dataset published in Nucleic Acids Research (2024). On theSindex it has a DataRank of 1.4, placing it in the top 14.7% of the data-sharing corpus. It has been cited 123 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 63/100.
Ranks in the top 15% for downstream scientific impact
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.
“https://maayanlab.cloud/Harmonizome/”
The strongest identifier for the dataset is a URL (lab website), not a persistent identifier scheme such as DOI, Handle, or repository accession.
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 Harmonizome 3.0 database is available at: https://maayanlab.cloud/Harmonizome/”
The data are hosted on the Maayan Lab cloud server, a non-repository institutional website, not a dedicated data repository.
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 Harmonizome 3.0 database is available at: https://maayanlab.cloud/Harmonizome/”
The dataset identifier (URL) appears only in the body text of the Data availability section, 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 Harmonizome 3.0 database is available at: https://maayanlab.cloud/Harmonizome/ . The Harmonizome processed datasets are available in multiple formats at: https://maayanlab.cloud/Harmonizome/download/ . The Harmonizome data processing scripts are available at: https://github.com/MaayanLab/HarmonizomePythonScripts . A snapshot of the code of these processing scripts can be access from Zenodo at: https://doi.org/10.5281/zenodo.13971451 .”
The data-availability statement points to URLs on a lab website, not to a repository record with a persistent identifier, so it is a link to data but not a repository link.
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. Summary of datasets added to the Harmonizome 3.0 upgrade.”
The paper includes an itemised inventory of the datasets (Table 1), which is a structured description of the data. [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'
“The Harmonizome 3.0 database is available at: https://maayanlab.cloud/Harmonizome/”
The data availability statement provides a direct URL with no precondition, indicating unconditional access.
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 paper does not label the access level of the data (e.g., open access, restricted), so no access condition artefact exists. [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 Harmonizome data are derived from public omics resources and are not human-subject data requiring a gatekeeper; 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
The paper gives no statement about how long the data will be preserved or when they become available; only current availability is mentioned. [majority verdict 'no' (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'
“These triples are provided in Resource Description Framework (RDF), JavaScript Object Notation (JSON), and tab-separated values (TSV) file formats”
The named formats (RDF, JSON, TSV) are open, non-proprietary formats.
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
“attributes were mapped to community established ontologies and dictionaries. For example, this was done for chemicals, drugs, anatomical structures, cell types, cell lines, tissues, diseases, phenotypes and more.”
The paper explicitly states that attributes were mapped to community ontologies and dictionaries, indicating use of community standards. [majority verdict 'yes' (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'
“10.1093/nar/gkac1052”
The reference list includes DOIs for external resources (e.g., UniProt), which are qualified references to data the study depends on. [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 licence or reuse terms are stated for the data; the CC BY-NC licence 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'
“Harmonizome 3.0, a significant upgrade to the original Harmonizome database.”
The paper explicitly names the version 'Harmonizome 3.0' for the entire database.
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'
“The Harmonizome data processing scripts are available at: https://github.com/MaayanLab/HarmonizomePythonScripts . A snapshot of the code of these processing scripts can be access from Zenodo at: https://doi.org/10.5281/zenodo.13971451”
The paper provides both a GitHub URL and a Zenodo DOI for the code, which are machine-resolvable, versioned locators. [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)
“NIH [R01DK131525, OT2OD036435, OT2OD030160, U24CA264250, U24CA271114, RC2DK131995].”
The paper lists specific NIH grant numbers, which are award identifiers.
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
“Visualization of datasets with UMAP ... using the Scikit-learn library”— not found in the paper; verdict downgraded
The paper names specific software (Scikit-learn, UMAP, Neo4j, OpenAI) used to process and visualize 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
“Table 1. Summary of datasets added to the Harmonizome 3.0 upgrade.”
Variable-level definitions (dataset attributes, gene set sizes) are provided in a table inside the article, not in a separate documentation object 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
0.723
From this paper's citation signal
Citation Network Contribution
0.685
From 46 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.
NIH
Grant: R01DK131525
NIH
Grant: OT2OD036435
NIH
Grant: OT2OD030160
NIH
Grant: U24CA264250
NIH
Grant: U24CA271114
NIH
Grant: RC2DK131995
National Institutes of Health
Grant: 1U24CA271114-01
Proteogenomic translator for cancer biomarker discovery towards precision medicine
National Institutes of Health
Grant: 1RC2DK131995-01
Diabetes Data and Hypothesis Hub (D2H2)
National Institutes of Health
Grant: 1OT2OD036435-01
The CFDE Workbench
National Institutes of Health
Grant: 5U24CA224260-05
Knowledge Management Center for Illuminating the Druggable Genome
National Institutes of Health
Grant: 5R01DK131525-03
Elucidating the Molecular Mechanisms that Mediate DKD Progression in Patients Living with HIV
National Institutes of Health
Grant: 3OT2OD030160-01S2
The LINCS DCIC Engagement Plan with the CFDE
National Institutes of Health
Grant: 5U24CA264250-02
ARCHS4: Massive Mining of Publicly Available RNA Sequencing Data
FWCI
20.37
Citation Percentile
1.0%
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals