{"doi":"10.1038/s41467-024-54591-6","title":"Functional tissue units in the Human Reference Atlas","abstract":"Functional tissue units form the basic building blocks of organs and are important for understanding and modeling the healthy physiological function of the organ and changes that occur during disease states. In this comprehensive catalog of 22 anatomically based, nested functional tissue units from 10 healthy human organs, we document the definition, physical dimensions, blood vasculature connections, and cellular composition. All anatomy terms are mapped to the multi-species Uber-anatomy Ontology (Uberon) and cells are mapped to Cell Ontology to support computational access via standardized metadata. The catalog includes datasets, illustrations, and a large printable poster illustrating how the blood vasculature connects the 22 functional tissue units in 10 organs. All data and code are freely available. The work is part of an ongoing international effort to construct a Human Reference Atlas of the 37 trillion cells that make up the healthy human body.","journal":"Nature Communications","year":2025,"id":510576,"datarank":0.5377610795260434,"base_score":2.995732273553991,"endowment":2.995732273553991,"self_citation_contribution":0.4493598410330987,"citation_network_contribution":0.08840123849294472,"self_endowment_contribution":0.4493598410330987,"citer_contribution":0.08840123849294472,"corpus_percentile":63.81991181248549,"corpus_rank":4678,"citation_count":19,"citer_count":12,"citers_with_citation_signal":7,"citers_with_endowment":7,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9051,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":75.0,"fair_percentile":95.6282482421278,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":20958,"name":"Katy Börner","orcid":"0000-0002-3321-6137","position":1,"is_corresponding":false},{"id":556229,"name":"Bruce W. Herr","orcid":"0000-0002-6703-7647","position":2,"is_corresponding":false},{"id":303981,"name":"Ellen M. Quardokus","orcid":"0000-0001-7655-4833","position":3,"is_corresponding":false},{"id":1366970,"name":"Marcell Nagy","orcid":"0000-0001-5666-7777","position":4,"is_corresponding":false},{"id":1161229,"name":"Katherine S. Gustilo","orcid":"0000-0002-5574-4272","position":5,"is_corresponding":false},{"id":1173370,"name":"Rachel Bajema","orcid":"0000-0002-3775-8574","position":6,"is_corresponding":false},{"id":1367679,"name":"Elizabeth Maier","orcid":null,"position":7,"is_corresponding":false},{"id":1173371,"name":"Roland Molontay","orcid":"0000-0002-0666-5279","position":8,"is_corresponding":false},{"id":39725,"name":"Griffin M. Weber","orcid":"0000-0002-2597-881X","position":9,"is_corresponding":false},{"id":1173368,"name":"Supriya Bidanta","orcid":"0000-0002-2142-983X","position":0,"is_corresponding":true}],"reference_count":32,"raw_metadata":null,"created_at":"2026-07-19T02:47:36.538276Z","pmid":"39934102","pmcid":"PMC11814273","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":83.3333,"fair_a":81.25,"fair_i":100.0,"fair_r":33.3333,"fair_zscore":1.6051,"fair_rationale":{"fair_score":75.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":83.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The supplementary data can be found on Zenodo at https://doi.org/10.5281/zenodo.11477238","grounded":true,"rationale":"The paper gives a DOI (10.5281/zenodo.11477238) for the supplementary data, which is a persistent identifier. [majority verdict 'yes' (4/5 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":1.0,"verdict":"yes","evidence":"The supplementary data can be found on Zenodo at https://doi.org/10.5281/zenodo.11477238","grounded":true,"rationale":"Zenodo is named as a repository that holds the supplementary data; Zenodo is a recognised data repository.","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":0.5,"verdict":"partial","evidence":"All data is freely available via the HRA Portal at https://humanatlas.io and the GitHub repository at https://github.com/cns-iu/hra-ftu-vccf-supporting-information. The supplementary data can be found on Zenodo at https://doi.org/10.5281/zenodo.11477238 and on GitHub at https://github.com/cns-iu/hra-ftu-vccf-supporting-information/tree/main/data.","grounded":false,"rationale":"The statement points at a repository record (Zenodo DOI) and names repositories, fitting Colavizza category 3. 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the paper does not name any gatekeeper of either kind.","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":0.5,"verdict":"partial","evidence":"All data is freely available via the HRA Portal at https://humanatlas.io and the GitHub repository at https://github.com/cns-iu/hra-ftu-vccf-supporting-information.","grounded":true,"rationale":"The paper states when the data become available (now) but does not state how long they persist.","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":100.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"The illustrations are saved in SVG, PNG, and AI format.","grounded":true,"rationale":"The paper names SVG and PNG, which are open, non-proprietary formats. [majority verdict 'yes' (4/5 passes agreed)]","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":1.0,"verdict":"yes","evidence":"All anatomy terms are mapped to the multi-species Uber-anatomy Ontology (Uberon) and cells are mapped to Cell Ontology","grounded":true,"rationale":"The paper explicitly names Uberon and Cell Ontology, which are community standards registered in FAIRsharing.","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":"Kidney Nephron UBERON:0001285","grounded":true,"rationale":"The paper uses Uberon IDs (e.g., UBERON:0001285) as identifiers for external ontology resources that the data are mapped to. [majority verdict 'yes' (4/5 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":33.33,"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 is named for the data; the article's CC-BY 4.0 licence applies to the article, not the dataset.","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":0.0,"verdict":"no","evidence":"HRA FTUs and experimental data visualizations were developed using an eight-step process: (1) consult the Anatomical Structure, Cell Types, and Biomarker (ASCT+B) tables to identify the anatomical structures and cell types present in an FTU; (2) identify FTU shape, dimensions, and cell types from experimental data on FTU geometries published in scholarly papers and histological visualizations; (3) a professional medical illustrator creates an initial pencil drawing of the FTU at the cellular level; (4) organ experts with extensive expertise in human anatomy and single-cell studies comment on the FTU properties and initial drawing; (5) a professional medical illustrator creates a vector-based drawing of the FTU guided by a Standard Operating Procedure (SOP) entitled \"Creating 2D Reference Illustrations for FTU\" and the \"Style Guide for Human Reference Atlas 2D Functional Tissue Unit (FTU) Illustrations\"; (6) organ experts review the drawings, metadata, and any existing disclaimers and suggest changes as needed which are implemented; (7) a crosswalk file is compiled that associates elements (anatomical structures and cell types) in the FTU vector file to their counterparts in the Anatomical Structures, Cell Types, and Biomarkers (ASCT+B) tables using the SOP titled \"Authoring Crosswalk Tables Between Functional Tissue Unit (FTU) Illustrations and ASCT+B Tables\"; and (8) the number of cells per cell type are recorded and the FTU 2D files is published with all metadata and the crosswalk via the HRA Portal as part of an HRA release.","grounded":false,"rationale":"The production process is described in generic terms without naming specific instruments, kits, or software versions for data generation. 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'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 is named for the data; the article's CC-BY 4.0 licence applies to the article, not the dataset.","gain":16.67,"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":"The supplementary data can be found on Zenodo at https://doi.org/10.5281/zenodo.11477238","why":"The dataset's identifier (DOI) appears only in the body text (Data availability section), not as a reference-list entry.","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":"All code is freely available at https://github.com/cns-iu/hra-ftu-vccf-supporting-information and a snapshot of the code was published on Zenodo at https://doi.org/10.5281/zenodo.11477238.","why":"The paper gives machine-resolvable locators (GitHub URL and Zenodo DOI) for the study's own code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","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":"partial","current":0.5,"evidence":"All data is freely available via the HRA Portal at https://humanatlas.io and the GitHub repository at https://github.com/cns-iu/hra-ftu-vccf-supporting-information. The supplementary data can be found on Zenodo at https://doi.org/10.5281/zenodo.11477238 and on GitHub at https://github.com/cns-iu/hra-ftu-vccf-supporting-information/tree/main/data.","why":"The statement points at a repository record (Zenodo DOI) and names repositories, fitting Colavizza category 3. 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'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":"no","current":0.0,"evidence":"HRA FTUs and experimental data visualizations were developed using an eight-step process: (1) consult the Anatomical Structure, Cell Types, and Biomarker (ASCT+B) tables to identify the anatomical structures and cell types present in an FTU; (2) identify FTU shape, dimensions, and cell types from experimental data on FTU geometries published in scholarly papers and histological visualizations; (3) a professional medical illustrator creates an initial pencil drawing of the FTU at the cellular level; (4) organ experts with extensive expertise in human anatomy and single-cell studies comment on the FTU properties and initial drawing; (5) a professional medical illustrator creates a vector-based drawing of the FTU guided by a Standard Operating Procedure (SOP) entitled \"Creating 2D Reference Illustrations for FTU\" and the \"Style Guide for Human Reference Atlas 2D Functional Tissue Unit (FTU) Illustrations\"; (6) organ experts review the drawings, metadata, and any existing disclaimers and suggest changes as needed which are implemented; (7) a crosswalk file is compiled that associates elements (anatomical structures and cell types) in the FTU vector file to their counterparts in the Anatomical Structures, Cell Types, and Biomarkers (ASCT+B) tables using the SOP titled \"Authoring Crosswalk Tables Between Functional Tissue Unit (FTU) Illustrations and ASCT+B Tables\"; and (8) the number of cells per cell type are recorded and the FTU 2D files is published with all metadata and the crosswalk via the HRA Portal as part of an HRA release.","why":"The production process is described in generic terms without naming specific instruments, kits, or software versions for data generation. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","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":"partial","current":0.5,"evidence":"together with a crosswalk file which maps the anatomy to the multispecies Uberon anatomy ontology and cell types to the Cell Ontology","why":"The paper states that a crosswalk file accompanies the data, which serves as a documentation object defining the mappings. 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NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All data is freely available via the HRA Portal at https://humanatlas.io and the GitHub repository at https://github.com/cns-iu/hra-ftu-vccf-supporting-information.","why":"The paper states when the data become available (now) but does not state how long they persist.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["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.","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.","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).","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.","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."],"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":"2026-07-20T11:56:43.429987Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}