Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage is a dataset published in Nature Methods (2025). On theSindex it has a DataRank of 0.802, placing it in the top 25.1% of the data-sharing corpus. It has been cited 33 times, with 24 citing works in its 1-hop citation network. Its calibrated FAIR score is 40/100.
Ranks in the top 25% 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.
“HRA data and code are available at the HRA Portal (https://humanatlas.io).”
The paper provides a web address (URL) for the data location, not a persistent identifier from a PID scheme. [majority verdict 'partial' (3/4 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'
“All HuBMAP data are available via the HuBMAP Data Portal at https://portal.hubmapconsortium.org.”— not found in the paper; verdict downgraded
The HuBMAP Data Portal is a named host but is not a curated repository listed in re3data/FAIRsharing (e.g., GEO, Zenodo). [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 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
“HRA data and code are available at the HRA Portal (https://humanatlas.io).”
The dataset identifier (a URL) appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (3/4 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
“All HuBMAP data are available via the HuBMAP Data Portal at https://portal.hubmapconsortium.org.”— not found in the paper; verdict downgraded
The data availability statement provides a URL to a portal rather than a specific repository record with an accession or DOI. [downgraded to 'no' — no verifiable quote from the paper]
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 sixth release of the HRA v.2.0 (December 2023) includes an anatomical structure systems graph which groups major organs into organ systems (for example, digestive system and reproductive system); three ASCT+B tables that represent the branching structures for the blood and lymph and the peripheral nervous system; and 29 ASCT+B tables that document the nested ‘part of’ structure of other organs (for example, kidney with cells that compose smaller and the subsequently large FTUs and organ parts) for a total of 33 ASCT+B tables.”
The dataset content is described in running prose with counts, not as a structured itemised inventory (table, section, or list). [majority verdict 'partial' (3/4 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 HuBMAP Data Portal provides open access to 2,332 datasets from 213 donors.”— not found in the paper; verdict downgraded
The paper explicitly states that the data are openly accessible with no precondition. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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 HuBMAP Data Portal provides open access to 2,332 datasets from 213 donors.”— not found in the paper; verdict downgraded
The paper explicitly labels the access level as 'open access' for the data in the HuBMAP Data Portal. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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 HuBMAP Data Portal provides open access to 2,332 datasets from 213 donors.”— not found in the paper; verdict downgraded
The paper states open access with no mention of a gatekeeper, institutional or personal, for sensitive data.
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 does not state how long this study's data will remain available; it only mentions that new releases are published every 6 months, which is an availability timing, not a persistence commitment. [majority verdict 'no' (2/4 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'
“Select data are also provided in a relational database and as comma-separated value (CSV) files.”
CSV is an open, non-proprietary, community-standard format.
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
“The sixth release of the HRA v.2.0 uses biological structure ontologies Uberon 2023-10-27 and FMA v.5.0.0 for anatomical structures; Cell Ontology (CL) v.2023-10-19 and PCL 2023-02-27 for cell types; HGNC v.2023-09-18, Ensembl Release 111, GeneCards v.5.19: 15 January 2024 and UniProt Release 2024_1 for biomarkers.”— not found in the paper; verdict downgraded
The paper names multiple community-standard ontologies and vocabularies (Uberon, CL, HGNC, etc.) used for the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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'
“Ensembl Release 111”
The paper includes a version identifier (Ensembl Release 111) for an external resource used in the study. [majority verdict 'yes' (3/4 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 named for the data in the paper.
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 sixth release of the HRA v.2.0 (December 2023) includes an anatomical structure systems graph...”— not found in the paper; verdict downgraded
The paper states a version token ('v.2.0') and release date for the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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 on three different GitHub organizations: (1) https://github.com/hubmapconsortium is the HuBMAP organization where HRA started; (2) https://github.com/cns-iu is the organization owned by the Cyberinfrastructure for Network Science Center at Indiana University and initial experimental HRA code starts here; and (3) https://github.com/x-atlas-consortia was created recently to host cross-consortia code, including hra-kg, hra-pop, hra-apps and hra-api.”— not found in the paper; verdict downgraded
The paper provides machine-resolvable code-forge URLs for the study's own code. [downgraded to 'partial' — no verifiable quote from the paper]
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)
“This research has been supported by the NIH Common Fund through the Office of Strategic Coordination/ Office of the NIH Director under awards: OT2OD033756 (K.B., Y.Z., G.M.W., Y.J., D.Q., A.B. and B.W.H.) and OT2OD026671 (K.B., G.M.W., Y.J., D.Q., A.B. and B.W.H.);”
The paper lists specific grant/award numbers (OT2OD033756, OT2OD026671) from the funder. [majority verdict 'yes' (3/4 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
“The HuBMAP sc/snRNA-seq pipeline, is built on the Salmon quasi-mapping method and performs gene expression quantification for intronic and exonic sequences, with downstream analysis using Scanpy and RNA velocity computation via scVelo.”— not found in the paper; verdict downgraded
The paper names specific software tools (Salmon, Scanpy, scVelo) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper]
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, data dictionary) is named as travelling with the data, nor are variable definitions provided inside the article. [majority verdict 'no' (3/4 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
0.529
From this paper's citation signal
Citation Network Contribution
0.274
From 12 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 24 citers.
U.S. Department of Health & Human Services | National Institutes of Health (NIH)
Grant: 3OT2OD033760
U.S. Department of Health & Human Services | National Institutes of Health (NIH)
Grant: HLU01148861
NIH HHS
Grant: OT2 OD026682
NCI NIH HHS
Grant: U24 CA268108
U.S. Department of Health & Human Services | National Institutes of Health (NIH)
Grant: U24DK135157
NIH HHS
Grant: OT2 OD026675
U.S. Department of Health & Human Services | National Institutes of Health (NIH)
Grant: OT2OD026671
U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)
Grant: RM1HG011014
U.S. Department of Health & Human Services | National Institutes of Health (NIH)
Grant: U2CDK114886
NIA NIH HHS
Grant: U54 AG075932
U.S. Department of Health & Human Services | National Institutes of Health (NIH)
Grant: U54HL165443
NCI NIH HHS
Grant: UH3 CA246594
NIH HHS
Grant: OT2 OD033761
NIDDK NIH HHS
Grant: U01 DK133090
NHLBI NIH HHS
Grant: U01 HL148861
U.S. Department of Health & Human Services | National Institutes of Health (NIH)
Grant: OT2OD026673
U.S. Department of Health & Human Services | National Institutes of Health (NIH)
Grant: 3OT2OD026682
U.S. Department of Health & Human Services | National Institutes of Health (NIH)
Grant: 3U54AG075936
BLRD VA
Grant: I01 BX007249
BLRD VA
Grant: IK6 BX005244
NIAMS NIH HHS
Grant: U54 AR081775
NIDDK NIH HHS
Grant: U54 DK134301
NIH HHS
Grant: OT2 OD033760
U.S. Department of Health & Human Services | National Institutes of Health (NIH)
Grant: 1OT2OD033761
U.S. Department of Health & Human Services | National Institutes of Health (NIH)
Grant: 1R03OD036499
NIH HHS
Grant: OT2 OD033759
NIA NIH HHS
Grant: U54 AG075936
NIH HHS
Grant: OT2 OD033756
NIH HHS
Grant: R03 OD036499
NHLBI NIH HHS
Grant: U54 HL165440
National Institutes of Health
Grant: 3U24CA268108-03S2
SenNet Supplement - 2 -FY 2024
National Institutes of Health
Grant: 3OT2OD033759-01S5
Flexible Hybrid Cloud Infrastructure for Seamless Integration and Use of Human Biomolecular Data and Reference Maps [1 of 5]
National Institutes of Health
Grant: 5U54AG075936-02
The Duke Senescent Cell Evaluations in Normal Tissues (SCENT) Mapping Center
National Institutes of Health
Grant: 1U54HL165443-01
The Human Lung BioMolecular Multi-Scale Atlas Program (HuBMAP-Lung)
National Institutes of Health
Grant: 3OT2OD026673-01S3
Comprehensive reference map construction, geolocation and data integration for HuBMAP HIVE
National Institutes of Health
Grant: 3OT2OD026682-01S1
Comprehensive, Flexible and FAIR Tools for the HuBMAP HIVE
National Institutes of Health
Grant: 1U2CDK114886-01
Central Hub for Kidney Precision Medicine
National Institutes of Health
Grant: 3OT2OD033756-01S1
3D Multiscale Biomolecular Human Reference Atlas Construction, Visualization and Usage [4 of 5]
National Institutes of Health
Grant: 3OT2OD033760-01S2
Comprehensive reference atlas construction, geolocation and data integration for HuBMAP HIVE [5 of 5]
National Institutes of Health
Grant: 3OT2OD026671-01S2
The Human Body Atlas: High-Resolution, Functional Mapping of Voxel, Vector, and Meta Datasets
National Institutes of Health
Grant: 1R03OD036499-01
Cell type harmonization of single cell data in HuBMAP and GTEx
National Institutes of Health
Grant: 1OT2OD033761-01
Computational tools for uniform processing and integration of human reference atlas data [2 of 5]
National Institutes of Health
Grant: 5RM1HG011014-02
Center for Integrated Cellular Analysis
National Institutes of Health
Grant: 1OT2OD026675-01
Flexible Hybrid Cloud Infrastructure for Seamless Management of HuBMAP Resources
National Institutes of Health
Grant: 5U24DK135157-02
National Institute of Diabetes and Digestive and Kidney Diseases ATLAS (D2K-ATLAS) Center as an accessible, comprehensive data portfolio for renal and genitourinary development and disease
FWCI
15.73
Citation Percentile
1.0%
Influential Citations
2
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals