{"doi":"10.1093/nar/gkac962","title":"The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain","abstract":"Scalable technologies to sequence the transcriptomes and epigenomes of single cells are transforming our understanding of cell types and cell states. The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative Cell Census Network (BICCN) is applying these technologies at unprecedented scale to map the cell types in the mammalian brain. In an effort to increase data FAIRness (Findable, Accessible, Interoperable, Reusable), the NIH has established repositories to make data generated by the BICCN and related BRAIN Initiative projects accessible to the broader research community. Here, we describe the Neuroscience Multi-Omic Archive (NeMO Archive; nemoarchive.org), which serves as the primary repository for genomics data from the BRAIN Initiative. Working closely with other BRAIN Initiative researchers, we have organized these data into a continually expanding, curated repository, which contains transcriptomic and epigenomic data from over 50 million brain cells, including single-cell genomic data from all of the major regions of the adult and prenatal human and mouse brains, as well as substantial single-cell genomic data from non-human primates. We make available several tools for accessing these data, including a searchable web portal, a cloud-computing interface for large-scale data processing (implemented on Terra, terra.bio), and a visualization and analysis platform, NeMO Analytics (nemoanalytics.org).","journal":"Nucleic Acids Research","year":2022,"id":236338,"datarank":1.0362689545933266,"base_score":4.2626798770413155,"endowment":4.2626798770413155,"self_citation_contribution":0.6394019815561974,"citation_network_contribution":0.3968669730371292,"self_endowment_contribution":0.6394019815561974,"citer_contribution":0.3968669730371292,"corpus_percentile":80.46723911193625,"corpus_rank":2526,"citation_count":70,"citer_count":22,"citers_with_citation_signal":18,"citers_with_endowment":18,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9559,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":68.75,"fair_percentile":91.13420972179762,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":59069,"name":"Ricky S. Adkins","orcid":"0000-0002-7983-5486","position":1,"is_corresponding":false},{"id":285750,"name":"Robert Carter","orcid":"0000-0003-0937-8141","position":2,"is_corresponding":false},{"id":857029,"name":"Elena Chrysostomou","orcid":null,"position":3,"is_corresponding":false},{"id":59071,"name":"Carlo Colantuoni","orcid":"0000-0001-6818-6380","position":4,"is_corresponding":false},{"id":19713,"name":"Jonathan Crabtree","orcid":"0000-0002-7286-5690","position":5,"is_corresponding":false},{"id":29019,"name":"Heather H. Creasy","orcid":"0000-0002-1369-6882","position":6,"is_corresponding":false},{"id":856313,"name":"Kylee Degatano","orcid":"0000-0002-0945-3300","position":7,"is_corresponding":false},{"id":482466,"name":"Victor Felix","orcid":"0000-0002-9773-0629","position":8,"is_corresponding":false},{"id":857030,"name":"Peter Gandt","orcid":null,"position":9,"is_corresponding":false},{"id":79796,"name":"Gwenn A. Garden","orcid":"0000-0002-8753-6515","position":10,"is_corresponding":false},{"id":29022,"name":"Michelle Giglio","orcid":"0000-0001-7628-5565","position":11,"is_corresponding":false},{"id":38338,"name":"Brian R. Herb","orcid":"0000-0002-5910-9647","position":12,"is_corresponding":false},{"id":539498,"name":"Farzaneh Khajouei","orcid":"0000-0002-0148-9122","position":13,"is_corresponding":false},{"id":516723,"name":"Elizabeth Kiernan","orcid":"0000-0002-6280-6072","position":14,"is_corresponding":false},{"id":59073,"name":"Carrie McCracken","orcid":"0000-0002-8038-9727","position":15,"is_corresponding":false},{"id":856314,"name":"Kennedy McDaniel","orcid":"0009-0000-0786-466X","position":16,"is_corresponding":false},{"id":70333,"name":"Suvarna Nadendla","orcid":"0000-0003-3643-281X","position":17,"is_corresponding":false},{"id":482467,"name":"Lance Nickel","orcid":"0000-0002-5836-3571","position":18,"is_corresponding":false},{"id":618854,"name":"Dustin Olley","orcid":"0000-0001-8685-0839","position":19,"is_corresponding":false},{"id":29139,"name":"Joshua Orvis","orcid":"0000-0002-5705-5710","position":20,"is_corresponding":false},{"id":69431,"name":"Joseph P. Receveur","orcid":"0000-0001-9157-3784","position":21,"is_corresponding":false},{"id":483707,"name":"Mike Schor","orcid":null,"position":22,"is_corresponding":false},{"id":256319,"name":"Shreyash Sonthalia","orcid":"0000-0003-1912-7901","position":23,"is_corresponding":false},{"id":35927,"name":"Timothy L. Tickle","orcid":"0000-0002-6592-6272","position":24,"is_corresponding":false},{"id":857031,"name":"Jessica Way","orcid":null,"position":25,"is_corresponding":false},{"id":38376,"name":"Ronna Hertzano","orcid":"0000-0002-8093-6567","position":26,"is_corresponding":false},{"id":29126,"name":"Anup A. Mahurkar","orcid":"0000-0002-4999-2296","position":27,"is_corresponding":false},{"id":38385,"name":"Owen R. White","orcid":"0000-0003-2407-7320","position":28,"is_corresponding":false},{"id":235850,"name":"Seth A. Ament","orcid":"0000-0001-6443-7509","position":0,"is_corresponding":true}],"reference_count":49,"raw_metadata":null,"created_at":"2026-07-19T00:21:58.728756Z","pmid":"36318260","pmcid":"PMC9825473","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":72.2222,"fair_a":68.75,"fair_i":80.0,"fair_r":37.5,"fair_zscore":1.3577,"fair_rationale":{"fair_score":68.75,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":72.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Data resources described in this manuscript are available in the NeMO Archive ( nemoarchive.org ) and NeMO Analytics ( nemoanalytics.org ).","grounded":true,"rationale":"The paper provides a web address (nemoarchive.org) for the data, not a PID-scheme string such as a DOI or repository accession. [majority verdict 'partial' (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 Neuroscience Multi-Omic Archive (NeMO Archive; nemoarchive.org), which serves as the primary repository for genomics data from the BRAIN Initiative.","grounded":true,"rationale":"The NeMO Archive is a proper data repository, named as the holder of the data. [majority verdict 'yes' (3/5 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":1.0,"verdict":"yes","evidence":"Data resources described in this manuscript are available in the NeMO Archive ( nemoarchive.org ) and NeMO Analytics ( nemoanalytics.org ).","grounded":true,"rationale":"The statement points to a repository (NeMO Archive) and provides a URL, which is a link to archived data in a public repository (Colavizza category 3). [majority verdict 'yes' (4/5 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":"Figure 1. NeMO Archive data inventory. (A) Growth of data storage in the NeMO Archive over time. (B) Counts of cells assayed by each transcriptomic or epigenomic technology. (C) Counts of cells for each species. Y-axes in panels B and C are on a log-scale.","grounded":false,"rationale":"The paper includes a figure caption that itemises the data inventory, providing a structured description of the dataset's contents. [downgraded to 'partial' — no verifiable quote from the paper] [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":"Data resources described in this manuscript are available in the NeMO Archive ( nemoarchive.org ) and NeMO Analytics ( nemoanalytics.org ).","grounded":true,"rationale":"The dataset identifier (URL) appears only in the body text of the data availability statement, not as a reference-list entry. [majority verdict 'partial' (4/5 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":"Data resources described in this manuscript are available in the NeMO Archive ( nemoarchive.org ) and NeMO Analytics ( nemoanalytics.org ).","grounded":true,"rationale":"The data availability statement provides a route to the data with no stated precondition; the paper also notes that no BICCN data are embargoed. [majority verdict 'yes' (4/5 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":"Data resources described in this manuscript are available in the NeMO Archive ( nemoarchive.org ) and NeMO Analytics ( nemoanalytics.org ).","grounded":true,"rationale":"The paper states where the data can be obtained but does not apply an explicit access-level label such as 'open access' or 'freely available'. [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":"the restricted incoming area for data requiring consented access (including controlled access human data)","grounded":true,"rationale":"The paper mentions a restricted area for human data but does not name a specific gatekeeper for the data described in this manuscript; the data availability statement gives a link without a gatekeeper.","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 majority of the data are being released to the research community prior to publication","grounded":true,"rationale":"The paper states when the data become available (prior to publication) but says nothing about how long they persist. [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":80.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"raw data consisting of FASTQ files","grounded":true,"rationale":"FASTQ is an open, community-standard format named for the 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":0.5,"verdict":"partial","evidence":"We are working to implement the use of standard ontologies and controlled vocabularies including NCBI Taxonomy, OBI, EDAM, Uberon","grounded":false,"rationale":"The paper names several community data/metadata standards (ontologies and controlled vocabularies) that are applied to the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":"RRID:SCR_018908","grounded":true,"rationale":"The paper provides an RRID for the Optimus pipeline, which is an identifier for a resource other than the paper's own dataset. [majority verdict 'yes' (3/5 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":37.5,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper mentions a Creative Commons Attribution License for the article itself, but does not state a license 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":0.5,"verdict":"partial","evidence":"Single-cell and single-nucleus 10× Genomics transcriptomic read-level data were processed to generate exon/intron counts using the Optimus pipeline (RRID:SCR_018908).","grounded":false,"rationale":"The paper names specific instruments and software (10× Genomics, Optimus pipeline) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":"The paper does not mention any README, data dictionary, or codebook that accompanies the deposited data. [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":0.5,"verdict":"partial","evidence":"As of 10 August 2022, the archive contains 383.1 terabytes of data","grounded":true,"rationale":"The paper provides a date that pins the snapshot of the data, but does not give a version token.","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 portal client ( https://github.com/IGS/portal_client )","grounded":true,"rationale":"The paper gives a GitHub URL for the portal client, which is a machine-resolvable locator for the study's 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":"National Institutes of Health [R24 MH114788 to O.R.W., R24 MH114815 to O.R.W., R.H., UM1 DA052244 to O.R.W., R01 DC019370 to R.H.].","grounded":true,"rationale":"The paper provides specific grant numbers for the funding.","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":"The paper mentions a Creative Commons Attribution License for the article itself, but does not state a license for the data.","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":"Data resources described in this manuscript are available in the NeMO Archive ( nemoarchive.org ) and NeMO Analytics ( nemoanalytics.org ).","why":"The paper provides a web address (nemoarchive.org) for the data, not a PID-scheme string such as a DOI or repository accession. [majority verdict 'partial' (4/5 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":"Data resources described in this manuscript are available in the NeMO Archive ( nemoarchive.org ) and NeMO Analytics ( nemoanalytics.org ).","why":"The dataset identifier (URL) appears only in the body text of the data availability statement, not as a reference-list entry. [majority verdict 'partial' (4/5 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":"partial","current":0.5,"evidence":"As of 10 August 2022, the archive contains 383.1 terabytes of data","why":"The paper provides a date that pins the snapshot of the data, but does not give a version token.","gain":2.08,"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":"Figure 1. NeMO Archive data inventory. (A) Growth of data storage in the NeMO Archive over time. (B) Counts of cells assayed by each transcriptomic or epigenomic technology. (C) Counts of cells for each species. Y-axes in panels B and C are on a log-scale.","why":"The paper includes a figure caption that itemises the data inventory, providing a structured description of the dataset's contents. [downgraded to 'partial' — no verifiable quote from the paper] [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":"Data resources described in this manuscript are available in the NeMO Archive ( nemoarchive.org ) and NeMO Analytics ( nemoanalytics.org ).","why":"The paper states where the data can be obtained but does not apply an explicit access-level label such as 'open access' or 'freely available'. [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":"partial","current":0.5,"evidence":"We are working to implement the use of standard ontologies and controlled vocabularies including NCBI Taxonomy, OBI, EDAM, Uberon","why":"The paper names several community data/metadata standards (ontologies and controlled vocabularies) that are applied to the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":"Single-cell and single-nucleus 10× Genomics transcriptomic read-level data were processed to generate exon/intron counts using the Optimus pipeline (RRID:SCR_018908).","why":"The paper names specific instruments and software (10× Genomics, Optimus pipeline) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":"no","current":0.0,"evidence":null,"why":"The paper does not mention any README, data dictionary, or codebook that accompanies the deposited data. [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":"the restricted incoming area for data requiring consented access (including controlled access human data)","why":"The paper mentions a restricted area for human data but does not name a specific gatekeeper for the data described in this manuscript; the data availability statement gives a link without a gatekeeper.","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 majority of the data are being released to the research community prior to publication","why":"The paper states when the data become available (prior to publication) but says nothing about how long they persist. [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.","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).","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":"2026-07-20T11:12:20.186181Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}