{"doi":"10.1038/s41592-024-02563-5","title":"Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage","abstract":"The Human BioMolecular Atlas Program (HuBMAP) aims to construct a 3D Human Reference Atlas (HRA) of the healthy adult body. Experts from 20+ consortia collaborate to develop a Common Coordinate Framework (CCF), knowledge graphs and tools that describe the multiscale structure of the human body (from organs and tissues down to cells, genes and biomarkers) and to use the HRA to characterize changes that occur with aging, disease and other perturbations. HRA v.2.0 covers 4,499 unique anatomical structures, 1,195 cell types and 2,089 biomarkers (such as genes, proteins and lipids) from 33 ASCT+B tables and 65 3D Reference Objects linked to ontologies. New experimental data can be mapped into the HRA using (1) cell type annotation tools (for example, Azimuth), (2) validated antibody panels or (3) by registering tissue data spatially. 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[majority verdict 'partial' (3/4 passes agreed)]","anchors":["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'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"All HuBMAP data are available via the HuBMAP Data Portal at https://portal.hubmapconsortium.org.","grounded":false,"rationale":"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)]","anchors":["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"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"All HuBMAP data are available via the HuBMAP Data Portal at https://portal.hubmapconsortium.org.","grounded":false,"rationale":"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]","anchors":["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"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"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.","grounded":true,"rationale":"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)]","anchors":["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'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"HRA data and code are available at the HRA Portal (https://humanatlas.io).","grounded":true,"rationale":"The dataset identifier (a URL) appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (3/4 passes agreed)]","anchors":["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'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":37.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The HuBMAP Data Portal provides open access to 2,332 datasets from 213 donors.","grounded":false,"rationale":"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)]","anchors":["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'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The HuBMAP Data Portal provides open access to 2,332 datasets from 213 donors.","grounded":false,"rationale":"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)]","anchors":["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"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"The HuBMAP Data Portal provides open access to 2,332 datasets from 213 donors.","grounded":false,"rationale":"The paper states open access with no mention of a gatekeeper, institutional or personal, for sensitive data.","anchors":["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"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"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)]","anchors":["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'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":80.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Select data are also provided in a relational database and as comma-separated value (CSV) files.","grounded":true,"rationale":"CSV is an open, non-proprietary, community-standard format.","anchors":["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"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"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.","grounded":false,"rationale":"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)]","anchors":["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'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"Ensembl Release 111","grounded":true,"rationale":"The paper includes a version identifier (Ensembl Release 111) for an external resource used in the study. [majority verdict 'yes' (3/4 passes agreed)]","anchors":["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'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":29.17,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No licence or reuse terms are named for the data in the paper.","anchors":["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'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"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.","grounded":false,"rationale":"The paper names specific software tools (Salmon, Scanpy, scVelo) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper]","anchors":["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"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"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)]","anchors":["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"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"The sixth release of the HRA v.2.0 (December 2023) includes an anatomical structure systems graph...","grounded":false,"rationale":"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)]","anchors":["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'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"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.","grounded":false,"rationale":"The paper provides machine-resolvable code-forge URLs for the study's own code. [downgraded to 'partial' — no verifiable quote from the paper]","anchors":["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)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"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.);","grounded":true,"rationale":"The paper lists specific grant/award numbers (OT2OD033756, OT2OD026671) from the funder. [majority verdict 'yes' (3/4 passes agreed)]","anchors":["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"],"scored":true,"signal":null}]}},"actions":[{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All HuBMAP data are available via the HuBMAP Data Portal at https://portal.hubmapconsortium.org.","why":"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)]","gain":16.67,"priority":"essential","scored":true},{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No licence or reuse terms are named for the data in the paper.","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"HRA data and code are available at the HRA Portal (https://humanatlas.io).","why":"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)]","gain":8.33,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The HuBMAP Data Portal provides open access to 2,332 datasets from 213 donors.","why":"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)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"HRA data and code are available at the HRA Portal (https://humanatlas.io).","why":"The dataset identifier (a URL) appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (3/4 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"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.","why":"The paper provides machine-resolvable code-forge URLs for the study's own code. [downgraded to 'partial' — no verifiable quote from the paper]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The sixth release of the HRA v.2.0 (December 2023) includes an anatomical structure systems graph...","why":"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)]","gain":2.08,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All HuBMAP data are available via the HuBMAP Data Portal at https://portal.hubmapconsortium.org.","why":"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]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"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.","why":"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)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The HuBMAP Data Portal provides open access to 2,332 datasets from 213 donors.","why":"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)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"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.","why":"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)]","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"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.","why":"The paper names specific software tools (Salmon, Scanpy, scVelo) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"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)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The HuBMAP Data Portal provides open access to 2,332 datasets from 213 donors.","why":"The paper states open access with no mention of a gatekeeper, institutional or personal, for sensitive data.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"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)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:32:28.427842Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}