{"doi":"10.1038/s41586-024-08172-8","title":"An integrated transcriptomic cell atlas of human neural organoids","abstract":"Human neural organoids, generated from pluripotent stem cells in vitro, are useful tools to study human brain development, evolution and disease. However, it is unclear which parts of the human brain are covered by existing protocols, and it has been difficult to quantitatively assess organoid variation and fidelity. Here we integrate 36 single-cell transcriptomic datasets spanning 26 protocols into one integrated human neural organoid cell atlas totalling more than 1.7 million cells<sup>1-26</sup>. Mapping to developing human brain references<sup>27-30</sup> shows primary cell types and states that have been generated in vitro, and estimates transcriptomic similarity between primary and organoid counterparts across protocols. We provide a programmatic interface to browse the atlas and query new datasets, and showcase the power of the atlas to annotate organoid cell types and evaluate new organoid protocols. Finally, we show that the atlas can be used as a diverse control cohort to annotate and compare organoid models of neural disease, identifying genes and pathways that may underlie pathological mechanisms with the neural models. The human neural organoid cell atlas will be useful to assess organoid fidelity, characterize perturbed and diseased states and facilitate protocol development.","journal":"Nature","year":2024,"id":10855,"datarank":2.0675138335398495,"base_score":4.852030263919617,"endowment":4.852030263919617,"self_citation_contribution":0.7278045395879427,"citation_network_contribution":1.3397092939519066,"self_endowment_contribution":0.7278045395879427,"citer_contribution":1.3397092939519066,"corpus_percentile":89.65730641293416,"corpus_rank":1338,"citation_count":127,"citer_count":100,"citers_with_citation_signal":62,"citers_with_endowment":62,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8956,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-11-20","fair_score":66.6667,"fair_percentile":86.48731274839498,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":12138,"name":"Leander Dony","orcid":"0000-0001-5697-6991","position":1,"is_corresponding":false},{"id":40551,"name":"Jonas Simon Fleck","orcid":"0000-0002-4686-7254","position":2,"is_corresponding":false},{"id":22110,"name":"Artur Szalata","orcid":"0000-0001-8413-234X","position":3,"is_corresponding":false},{"id":40552,"name":"Katelyn X. Li","orcid":"0000-0001-8799-0534","position":4,"is_corresponding":false},{"id":40553,"name":"Irena Slišković","orcid":"0009-0003-6222-7657","position":5,"is_corresponding":false},{"id":40555,"name":"Malgorzata Santel","orcid":"0009-0006-4947-8509","position":7,"is_corresponding":false},{"id":40556,"name":"Alexander Atamian","orcid":"0009-0004-5525-2018","position":8,"is_corresponding":false},{"id":40557,"name":"Giorgia Quadrato","orcid":"0000-0003-0717-4874","position":9,"is_corresponding":false},{"id":40558,"name":"Jieran Sun","orcid":"0000-0002-7996-3840","position":10,"is_corresponding":false},{"id":40559,"name":"Sergiu P. Pașca","orcid":"0000-0002-3216-3248","position":11,"is_corresponding":false},{"id":40560,"name":"Human Cell Atlas Organoid Biological Network","orcid":null,"position":12,"is_corresponding":false},{"id":40561,"name":"Neal D. Amin","orcid":"0000-0003-2027-1329","position":13,"is_corresponding":false},{"id":40562,"name":"Kevin W. Kelley","orcid":null,"position":14,"is_corresponding":false},{"id":40563,"name":"Taylor Bertucci","orcid":"0009-0008-1017-6807","position":15,"is_corresponding":false},{"id":40564,"name":"Sally Temple","orcid":"0000-0001-7301-783X","position":16,"is_corresponding":false},{"id":40565,"name":"Kathryn R. Bowles","orcid":null,"position":17,"is_corresponding":false},{"id":40567,"name":"Emanuele Villa","orcid":null,"position":19,"is_corresponding":false},{"id":40568,"name":"Giuseppe Testa","orcid":"0000-0002-9104-0918","position":20,"is_corresponding":false},{"id":13070,"name":"Cristiana Cruceanu","orcid":"0000-0002-7799-5531","position":21,"is_corresponding":false},{"id":5365,"name":"Elisabeth B. Binder","orcid":"0000-0001-7088-6618","position":22,"is_corresponding":false},{"id":29631,"name":"J. Gray Camp","orcid":"0000-0003-3295-1225","position":23,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":24,"is_corresponding":false},{"id":29636,"name":"Barbara Treutlein","orcid":"0000-0002-3299-5597","position":25,"is_corresponding":false},{"id":40569,"name":"Hsiu‐Chuan Lin","orcid":"0000-0001-9587-6483","position":26,"is_corresponding":false},{"id":40570,"name":"Carlo Emanuele Villa","orcid":"0000-0002-1208-3160","position":27,"is_corresponding":false},{"id":40550,"name":"Zhisong He","orcid":"0000-0002-1502-4801","position":0,"is_corresponding":true}],"reference_count":100,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"39567792","pmcid":"PMC11578878","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"hybrid","license":"cc-by-nc-nd","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":83.3333,"fair_a":68.75,"fair_i":20.0,"fair_r":41.6667,"fair_zscore":1.2752,"fair_rationale":{"fair_score":66.67,"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 integrated HNOCA data is available at Zenodo (10.5281/zenodo.11203684) 100","grounded":true,"rationale":"The paper gives a DOI for the dataset.","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 integrated HNOCA data is available at Zenodo (10.5281/zenodo.11203684) 100","grounded":true,"rationale":"Zenodo is named as a repository holding the data.","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":1.0,"verdict":"yes","evidence":"The integrated HNOCA data is available at Zenodo (10.5281/zenodo.11203684) 100 and the CellxGene Discover Census ( https://cellxgene.cziscience.com/collections/de379e5f-52d0-498c-9801-0f850823c847 ).","grounded":true,"rationale":"The statement points at a repository record with a DOI and a repository URL. [majority verdict 'yes' (3/5 passes agreed)]","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":"Here we integrate 36 single-cell transcriptomic datasets spanning 26 protocols into one integrated human neural organoid cell atlas totalling more than 1.7 million cells 1 – 26 .","grounded":true,"rationale":"The dataset content and size are stated in running prose only, without an itemised inventory. [majority verdict 'partial' (3/5 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":"He, Z. Dony, L. & Fleck, J. S. An integrated transcriptomic cell atlas of human neural organoids: cleaned datasets. Zenodo 10.5281/zenodo.11203684 (2023).","grounded":false,"rationale":"The dataset appears as a reference-list entry in the references section. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":68.75,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The integrated HNOCA data is available at Zenodo (10.5281/zenodo.11203684) 100 and the CellxGene Discover Census ( https://cellxgene.cziscience.com/collections/de379e5f-52d0-498c-9801-0f850823c847 ).","grounded":true,"rationale":"The text gives a route to the data with no stated precondition.","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 integrated HNOCA data is available at Zenodo (10.5281/zenodo.11203684) 100 and the CellxGene Discover Census ( https://cellxgene.cziscience.com/collections/de379e5f-52d0-498c-9801-0f850823c847 ).","grounded":true,"rationale":"The paper describes the action of accessing the data at the URLs but does not apply an explicit access-level label from the standard vocabulary. [majority verdict 'partial' (4/5 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":null,"grounded":false,"rationale":"The data are not sensitive or human-subject, and no gatekeeper of any kind is mentioned.","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":"The integrated HNOCA data is available at Zenodo (10.5281/zenodo.11203684) 100 and the CellxGene Discover Census ( https://cellxgene.cziscience.com/collections/de379e5f-52d0-498c-9801-0f850823c847 ).","grounded":true,"rationale":"The paper states that the data are currently available but does not specify how long they will persist, so it is an availability-timing statement only. [majority verdict 'partial' (4/5 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":20.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file format is named for the released data.","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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No data or metadata community standard is named as applied to the released dataset. [majority verdict 'no' (4/5 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":"Braun E Comprehensive cell atlas of the first-trimester developing human brain Science 2023 382 eadf1226 10.1126/science.adf1226","grounded":true,"rationale":"The paper includes a reference to an external resource with a DOI (the primary brain atlas).","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":41.67,"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 terms document is named for the data.","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":1.0,"verdict":"yes","evidence":"We used scPoli 45 for label-aware data integration","grounded":true,"rationale":"The text names a specific software tool (scPoli) used to produce the data. [majority verdict 'yes' (4/5 passes agreed)]","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) is mentioned as accompanying the data, and no variable-definition table exists inside the article for the integrated dataset. [majority verdict 'no' (4/5 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No version token or date is stated for the snapshot of the data.","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":1.0,"verdict":"yes","evidence":"The HNOCA-tools package provides a Python interface for annotation, reference mapping and central downstream analysis steps and is available at https://github.com/devsystemslab/HNOCA-tools .","grounded":true,"rationale":"A machine-resolvable code repository URL is given for the study's own code.","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 work was supported by Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation (grant nos. CZF2019-002440 and CZF2021-237566, to J.G.C. and B.T.).","grounded":true,"rationale":"An award/grant number (CZF2019-002440) is attached to a named funder. [majority verdict 'yes' (4/5 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":"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 terms document is named for the data.","gain":16.67,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format is named for the released data.","gain":8.33,"priority":"important","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":"He, Z. Dony, L. & Fleck, J. S. An integrated transcriptomic cell atlas of human neural organoids: cleaned datasets. Zenodo 10.5281/zenodo.11203684 (2023).","why":"The dataset appears as a reference-list entry in the references section. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","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":"no","current":0.0,"evidence":null,"why":"No version token or date is stated for the snapshot of the data.","gain":4.17,"priority":"useful","scored":true},{"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":"Here we integrate 36 single-cell transcriptomic datasets spanning 26 protocols into one integrated human neural organoid cell atlas totalling more than 1.7 million cells 1 – 26 .","why":"The dataset content and size are stated in running prose only, without an itemised inventory. [majority verdict 'partial' (3/5 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 integrated HNOCA data is available at Zenodo (10.5281/zenodo.11203684) 100 and the CellxGene Discover Census ( https://cellxgene.cziscience.com/collections/de379e5f-52d0-498c-9801-0f850823c847 ).","why":"The paper describes the action of accessing the data at the URLs but does not apply an explicit access-level label from the standard vocabulary. [majority verdict 'partial' (4/5 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":"no","current":0.0,"evidence":null,"why":"No data or metadata community standard is named as applied to the released dataset. [majority verdict 'no' (4/5 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":"no","current":0.0,"evidence":null,"why":"No documentation object (README, codebook) is mentioned as accompanying the data, and no variable-definition table exists inside the article for the integrated dataset. [majority verdict 'no' (4/5 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":null,"why":"The data are not sensitive or human-subject, and no gatekeeper of any kind is mentioned.","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":"partial","current":0.5,"evidence":"The integrated HNOCA data is available at Zenodo (10.5281/zenodo.11203684) 100 and the CellxGene Discover Census ( https://cellxgene.cziscience.com/collections/de379e5f-52d0-498c-9801-0f850823c847 ).","why":"The paper states that the data are currently available but does not specify how long they will persist, so it is an availability-timing statement only. [majority verdict 'partial' (4/5 passes agreed)]","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.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","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.","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.","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."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:00:58.435847Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}