{"doi":"10.1126/sciadv.abn4965","title":"A reference tissue atlas for the human kidney","abstract":"Kidney Precision Medicine Project (KPMP) is building a spatially specified human kidney tissue atlas in health and disease with single-cell resolution. Here, we describe the construction of an integrated reference map of cells, pathways, and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 56 adult subjects. We use single-cell/nucleus transcriptomics, subsegmental laser microdissection transcriptomics and proteomics, near-single-cell proteomics, 3D and CODEX imaging, and spatial metabolomics to hierarchically identify genes, pathways, and cells. Integrated data from these different technologies coherently identify cell types/subtypes within different nephron segments and the interstitium. These profiles describe cell-level functional organization of the kidney following its physiological functions and link cell subtypes to genes, proteins, metabolites, and pathways. They further show that messenger RNA levels along the nephron are congruent with the subsegmental physiological activity. This reference atlas provides a framework for the classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.","journal":"Science Advances","year":2022,"id":232686,"datarank":4.096545257312077,"base_score":5.159055299214529,"endowment":5.159055299214529,"self_citation_contribution":0.7738582948821795,"citation_network_contribution":3.322686962429898,"self_endowment_contribution":0.7738582948821795,"citer_contribution":3.322686962429898,"corpus_percentile":94.55403419200124,"corpus_rank":705,"citation_count":173,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9386,"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":50.0,"fair_percentile":62.702537450321,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":5957,"name":"Rachel Sealfon","orcid":"0000-0002-3007-4698","position":1,"is_corresponding":false},{"id":250809,"name":"Rajasree Menon","orcid":"0000-0001-6280-9639","position":2,"is_corresponding":false},{"id":307583,"name":"Michael T. Eadon","orcid":"0000-0003-3066-2876","position":3,"is_corresponding":false},{"id":38318,"name":"Blue B. Lake","orcid":"0000-0002-8637-9044","position":4,"is_corresponding":false},{"id":308059,"name":"Becky Steck","orcid":"0000-0001-7565-4904","position":5,"is_corresponding":false},{"id":845036,"name":"Kavya Anjani","orcid":null,"position":6,"is_corresponding":false},{"id":407214,"name":"Samir V. Parikh","orcid":"0000-0001-7023-525X","position":7,"is_corresponding":false},{"id":2702,"name":"Tara K. Sigdel","orcid":"0000-0001-8448-0328","position":8,"is_corresponding":false},{"id":321342,"name":"Guanshi Zhang","orcid":"0000-0001-6557-4521","position":9,"is_corresponding":false},{"id":475284,"name":"Dušan Veličković","orcid":"0000-0001-7945-9620","position":10,"is_corresponding":false},{"id":388336,"name":"Daria Barwinska","orcid":"0000-0002-0776-3030","position":11,"is_corresponding":false},{"id":105897,"name":"Theodore Alexandrov","orcid":"0000-0001-9464-6125","position":12,"is_corresponding":false},{"id":435353,"name":"Deján Dobi","orcid":"0000-0001-6780-7712","position":13,"is_corresponding":false},{"id":563041,"name":"Priyanka Rashmi","orcid":"0000-0001-5101-3379","position":14,"is_corresponding":false},{"id":255141,"name":"Edgar A. Otto","orcid":"0000-0002-2387-9973","position":15,"is_corresponding":false},{"id":843798,"name":"Miguel Rivera","orcid":"0000-0003-1714-1152","position":16,"is_corresponding":false},{"id":563042,"name":"Michael Rose","orcid":"0000-0001-8661-5134","position":17,"is_corresponding":false},{"id":308063,"name":"Christopher Anderton","orcid":"0000-0002-6170-1033","position":18,"is_corresponding":false},{"id":407213,"name":"John P. Shapiro","orcid":"0000-0001-6698-2340","position":19,"is_corresponding":false},{"id":563043,"name":"Annapurna Pamreddy","orcid":"0000-0002-5284-0808","position":20,"is_corresponding":false},{"id":388338,"name":"Seth Winfree","orcid":"0000-0002-2396-5871","position":21,"is_corresponding":false},{"id":573720,"name":"Yuguang Xiong","orcid":"0000-0001-5221-6266","position":22,"is_corresponding":false},{"id":90652,"name":"Yongqun He","orcid":"0000-0001-9189-9661","position":23,"is_corresponding":false},{"id":231201,"name":"Ian H. de Boer","orcid":"0000-0003-1571-7592","position":24,"is_corresponding":false},{"id":247035,"name":"Jeffrey B. Hodgin","orcid":"0000-0003-0534-3048","position":25,"is_corresponding":false},{"id":237302,"name":"Laura Barisoni","orcid":"0000-0003-0848-9683","position":26,"is_corresponding":false},{"id":96845,"name":"Abhijit S. Naik","orcid":"0000-0003-1602-9425","position":27,"is_corresponding":false},{"id":292969,"name":"Kumar Sharma","orcid":"0000-0002-7550-8525","position":28,"is_corresponding":false},{"id":2709,"name":"Minnie Sarwal","orcid":"0000-0003-1212-3959","position":29,"is_corresponding":false},{"id":323507,"name":"Kun Zhang","orcid":"0000-0002-7596-5224","position":30,"is_corresponding":false},{"id":54241,"name":"Jonathan Himmelfarb","orcid":"0000-0002-3319-1224","position":31,"is_corresponding":false},{"id":284163,"name":"Brad H. Rovin","orcid":"0000-0001-5639-0210","position":32,"is_corresponding":false},{"id":307590,"name":"Tarek M. El‐Achkar","orcid":"0000-0003-4645-3614","position":33,"is_corresponding":false},{"id":435354,"name":"Zoltán Lászik","orcid":"0000-0003-0511-8764","position":34,"is_corresponding":false},{"id":263575,"name":"John Cijiang He","orcid":"0000-0002-1502-2849","position":35,"is_corresponding":false},{"id":307589,"name":"Pierre C. Dagher","orcid":"0000-0003-3321-5561","position":36,"is_corresponding":false},{"id":279574,"name":"M. Todd Valerius","orcid":"0000-0001-8143-9231","position":37,"is_corresponding":false},{"id":255147,"name":"Sanjay Jain","orcid":"0000-0003-2804-127X","position":38,"is_corresponding":false},{"id":356417,"name":"Lisa M. Satlin","orcid":"0000-0002-1744-1748","position":39,"is_corresponding":false},{"id":5951,"name":"Olga G. Troyanskaya","orcid":"0000-0002-5676-5737","position":40,"is_corresponding":false},{"id":5968,"name":"Matthias Kretzler","orcid":"0000-0003-4064-0582","position":41,"is_corresponding":false},{"id":330695,"name":"Ravi Iyengar","orcid":"0000-0002-7814-0180","position":42,"is_corresponding":false},{"id":284301,"name":"Evren U. Azeloglu","orcid":"0000-0001-6137-109X","position":43,"is_corresponding":false},{"id":257085,"name":"Kidney Precision Medicine Project","orcid":null,"position":44,"is_corresponding":false},{"id":308061,"name":"Jens Hansen","orcid":"0000-0002-1362-6534","position":0,"is_corresponding":true}],"reference_count":94,"raw_metadata":null,"created_at":"2026-07-19T00:21:18.683916Z","pmid":"35675394","pmcid":"PMC9176741","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":55.5556,"fair_a":50.0,"fair_i":20.0,"fair_r":50.0,"fair_zscore":0.6155,"fair_rationale":{"fair_score":50.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":55.56,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"DOI: 10.48698/z30t-0a62","grounded":false,"rationale":"The paper provides a DOI for the dataset, which is a persistent identifier scheme. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":"Gene Expression Omnibus","grounded":true,"rationale":"The paper names multiple repositories (GEO, MassIVE, Zenodo, KPMP Data Portal) as the holders of the data. [majority verdict 'yes' (4/5 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":0.5,"verdict":"partial","evidence":"All raw and processed data described in this manuscript are available through the KPMP Data Portal at kpmp.org (DOI: 10.48698/z30t-0a62) and Zenodo (DOI: 10.5281/zenodo.6410326).","grounded":false,"rationale":"The statement points to repositories with persistent identifiers, satisfying Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":"The raw transcriptomics data are also available on Gene Expression Omnibus with the accession IDs GSE163603, GSE121862, and GSE140989. Raw proteomics data are publicly available on MassIVE repository with the accession ID MSV000089251.","grounded":true,"rationale":"The description of the dataset is in running prose, not an itemised inventory. [majority verdict 'partial' (4/5 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":0.0,"verdict":"no","evidence":"All raw and processed data described in this manuscript are available through the KPMP Data Portal at kpmp.org (DOI: 10.48698/z30t-0a62) and Zenodo (DOI: 10.5281/zenodo.6410326).","grounded":false,"rationale":"Dataset identifiers appear only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":50.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All raw and processed data described in this manuscript are available through the KPMP Data Portal at kpmp.org (DOI: 10.48698/z30t-0a62) and Zenodo (DOI: 10.5281/zenodo.6410326).","grounded":false,"rationale":"The data are stated to be available without any precondition. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":1.0,"verdict":"yes","evidence":"Raw proteomics data are publicly available on MassIVE repository with the accession ID MSV000089251.","grounded":true,"rationale":"The paper labels the access level as 'publicly available' for the raw proteomics data. [majority verdict 'yes' (3/5 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":"All raw and processed data described in this manuscript are available through the KPMP Data Portal at kpmp.org (DOI: 10.48698/z30t-0a62) and Zenodo (DOI: 10.5281/zenodo.6410326).","grounded":false,"rationale":"No gatekeeper is named; the data are stated to be openly available.","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":"All raw and processed data described in this manuscript are available through the KPMP Data Portal at kpmp.org (DOI: 10.48698/z30t-0a62) and Zenodo (DOI: 10.5281/zenodo.6410326).","grounded":false,"rationale":"No persistence commitment or retention period is stated; only current availability is mentioned. [majority verdict 'no' (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 community data standard (e.g., MIAME, BIDS) is named for the dataset. [majority verdict 'no' (2/5 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":"GSE114156","grounded":true,"rationale":"The paper references an external dataset (GSE114156) from the literature. [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":50.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No license is explicitly attached to the data; the article's CC BY-NC license does not apply to the data. [majority verdict 'no' (3/5 passes agreed)]","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":"Sequencing was conducted on an Illumina HiSeq 4000.","grounded":true,"rationale":"The paper names specific instruments and software used for data generation.","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 codebook, README, or data dictionary is mentioned as accompanying the data.","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":1.0,"verdict":"yes","evidence":"DOI: 10.5281/zenodo.6410326","grounded":true,"rationale":"The Zenodo DOI is versioned, providing a snapshot identifier. [majority verdict 'yes' (3/5 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":1.0,"verdict":"yes","evidence":"Fully annotated scripts and readme files that can be used to generate all the main figures in this manuscript are freely available at the KPMP GitHub portal (https://github.com/KPMP/Reference-Tissue-Cell-Atlas-Manuscript-2022).","grounded":true,"rationale":"The paper provides a GitHub URL for the code, which is a machine-resolvable locator.","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":"UH3 DK114923","grounded":true,"rationale":"The paper lists NIH grant numbers, which are award identifiers.","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 license is explicitly attached to the data; the article's CC BY-NC license does not apply to the data. [majority verdict 'no' (3/5 passes agreed)]","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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"DOI: 10.48698/z30t-0a62","why":"The paper provides a DOI for the dataset, which is a persistent identifier scheme. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All raw and processed data described in this manuscript are available through the KPMP Data Portal at kpmp.org (DOI: 10.48698/z30t-0a62) and Zenodo (DOI: 10.5281/zenodo.6410326).","why":"The data are stated to be available without any precondition. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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 proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All raw and processed data described in this manuscript are available through the KPMP Data Portal at kpmp.org (DOI: 10.48698/z30t-0a62) and Zenodo (DOI: 10.5281/zenodo.6410326).","why":"Dataset identifiers appear only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":8.33,"priority":"important","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 proteomics formats such as mzML or mzIdentML.","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_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 raw and processed data described in this manuscript are available through the KPMP Data Portal at kpmp.org (DOI: 10.48698/z30t-0a62) and Zenodo (DOI: 10.5281/zenodo.6410326).","why":"The statement points to repositories with persistent identifiers, satisfying Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","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 raw transcriptomics data are also available on Gene Expression Omnibus with the accession IDs GSE163603, GSE121862, and GSE140989. Raw proteomics data are publicly available on MassIVE repository with the accession ID MSV000089251.","why":"The description of the dataset is in running prose, not an itemised inventory. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","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 proteomics, describe the data with mzML or MIAPE.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No community data standard (e.g., MIAME, BIDS) is named for the dataset. [majority verdict 'no' (2/5 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 codebook, README, or data dictionary is mentioned as accompanying the data.","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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All raw and processed data described in this manuscript are available through the KPMP Data Portal at kpmp.org (DOI: 10.48698/z30t-0a62) and Zenodo (DOI: 10.5281/zenodo.6410326).","why":"No gatekeeper is named; the data are stated to be openly available.","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":"All raw and processed data described in this manuscript are available through the KPMP Data Portal at kpmp.org (DOI: 10.48698/z30t-0a62) and Zenodo (DOI: 10.5281/zenodo.6410326).","why":"No persistence commitment or retention period is stated; only current availability is mentioned. [majority verdict 'no' (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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","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 proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","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 proteomics formats such as mzML or mzIdentML."],"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":"2026-07-20T10:56:32.360973Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}