{"doi":"10.1126/science.adh1938","title":"A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex","abstract":"The molecular organization of the human neocortex historically has been studied in the context of its histological layers. However, emerging spatial transcriptomic technologies have enabled unbiased identification of transcriptionally defined spatial domains that move beyond classic cytoarchitecture. We used the Visium spatial gene expression platform to generate a data-driven molecular neuroanatomical atlas across the anterior-posterior axis of the human dorsolateral prefrontal cortex. Integration with paired single-nucleus RNA-sequencing data revealed distinct cell type compositions and cell-cell interactions across spatial domains. Using PsychENCODE and publicly available data, we mapped the enrichment of cell types and genes associated with neuropsychiatric disorders to discrete spatial domains.","journal":"Science","year":2024,"id":417451,"datarank":1.1551348188669657,"base_score":4.248495242049359,"endowment":4.248495242049359,"self_citation_contribution":0.637274286307404,"citation_network_contribution":0.5178605325595615,"self_endowment_contribution":0.637274286307404,"citer_contribution":0.5178605325595615,"corpus_percentile":82.2232536551404,"corpus_rank":2299,"citation_count":69,"citer_count":44,"citers_with_citation_signal":31,"citers_with_endowment":31,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.881,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":66.6667,"fair_percentile":86.48731274839498,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":807086,"name":"Abby Spangler","orcid":"0000-0002-0028-9348","position":1,"is_corresponding":false},{"id":21391,"name":"Nicholas J. Eagles","orcid":"0000-0002-9808-5254","position":2,"is_corresponding":false},{"id":988304,"name":"Kelsey D. Montgomery","orcid":"0000-0001-8420-0138","position":3,"is_corresponding":false},{"id":60973,"name":"Sang Ho Kwon","orcid":"0000-0001-5328-0956","position":4,"is_corresponding":false},{"id":399554,"name":"Boyi Guo","orcid":"0000-0003-2950-2349","position":5,"is_corresponding":false},{"id":6420,"name":"Melissa Grant‐Peters","orcid":"0000-0003-0585-0971","position":6,"is_corresponding":false},{"id":988302,"name":"Heena R. Divecha","orcid":"0000-0002-1959-0675","position":7,"is_corresponding":false},{"id":988305,"name":"Madhavi Tippani","orcid":"0000-0002-6465-6418","position":8,"is_corresponding":false},{"id":825716,"name":"Chaichontat Sriworarat","orcid":"0000-0002-1917-3409","position":9,"is_corresponding":false},{"id":1159885,"name":"Annie B. Nguyen","orcid":"0000-0003-3842-6923","position":10,"is_corresponding":false},{"id":1159886,"name":"Prashanthi Ravichandran","orcid":"0000-0002-9364-175X","position":11,"is_corresponding":false},{"id":988303,"name":"Matthew N. Tran","orcid":"0000-0001-9694-7378","position":12,"is_corresponding":false},{"id":1159887,"name":"Arta Seyedian","orcid":"0000-0003-4141-4149","position":13,"is_corresponding":false},{"id":6265,"name":"Thomas M. Hyde","orcid":"0000-0002-8746-3037","position":14,"is_corresponding":false},{"id":6266,"name":"Joel E. Kleinman","orcid":"0000-0002-4210-6052","position":15,"is_corresponding":false},{"id":103605,"name":"Alexis Battle","orcid":"0000-0002-5287-627X","position":16,"is_corresponding":false},{"id":21457,"name":"Stephanie C. Page","orcid":"0000-0002-1951-7398","position":17,"is_corresponding":false},{"id":45812,"name":"Mina Ryten","orcid":"0000-0001-9520-6957","position":18,"is_corresponding":false},{"id":1437,"name":"Stephanie C. Hicks","orcid":"0000-0002-7858-0231","position":19,"is_corresponding":false},{"id":6260,"name":"Keri Martinowich","orcid":"0000-0002-5237-0789","position":20,"is_corresponding":false},{"id":21520,"name":"Leonardo Collado‐Torres","orcid":"0000-0003-2140-308X","position":21,"is_corresponding":false},{"id":21441,"name":"Kristen R. Maynard","orcid":"0000-0003-0031-8468","position":22,"is_corresponding":false},{"id":21362,"name":"Schahram Akbarian","orcid":"0000-0001-7700-0891","position":23,"is_corresponding":false},{"id":21363,"name":"Alexej Abyzov","orcid":"0000-0001-5405-6729","position":24,"is_corresponding":false},{"id":6730,"name":"Nadav Ahituv","orcid":"0000-0002-7434-8144","position":25,"is_corresponding":false},{"id":21364,"name":"Dhivya Arasappan","orcid":null,"position":26,"is_corresponding":false},{"id":21518,"name":"José Juan Almagro Armenteros","orcid":"0000-0003-0111-1362","position":27,"is_corresponding":false},{"id":21366,"name":"Brian J. Beliveau","orcid":"0000-0003-1314-3118","position":28,"is_corresponding":false},{"id":284407,"name":"Jaroslav Bendl","orcid":"0000-0001-9989-2720","position":29,"is_corresponding":false},{"id":6264,"name":"Sabina Berretta","orcid":"0000-0002-4057-7766","position":30,"is_corresponding":false},{"id":21519,"name":"Rahul Bharadwaj","orcid":"0000-0002-7749-8682","position":31,"is_corresponding":false},{"id":21368,"name":"Arjun Bhattacharya","orcid":"0000-0003-1196-4385","position":32,"is_corresponding":false},{"id":21369,"name":"Lucy Bicks","orcid":"0000-0002-9884-0133","position":33,"is_corresponding":false},{"id":21370,"name":"Kristen Brennand","orcid":"0000-0003-0993-5956","position":34,"is_corresponding":false},{"id":483481,"name":"Davide Capauto","orcid":"0000-0003-2156-0165","position":35,"is_corresponding":false},{"id":21371,"name":"Frances A. Champagne","orcid":"0000-0002-3922-084X","position":36,"is_corresponding":false},{"id":1199592,"name":"Tanima Chatterjee","orcid":"0000-0001-8956-6569","position":37,"is_corresponding":false},{"id":21373,"name":"Chris Chatzinakos","orcid":"0000-0003-0557-9501","position":38,"is_corresponding":false},{"id":21374,"name":"Yuhang Chen","orcid":"0000-0001-9906-4108","position":39,"is_corresponding":false},{"id":279223,"name":"H. Isaac Chen","orcid":"0000-0002-7431-6046","position":40,"is_corresponding":false},{"id":21376,"name":"Yuyan Cheng","orcid":"0000-0003-4647-4917","position":41,"is_corresponding":false},{"id":12288,"name":"Lijun Cheng","orcid":"0000-0001-7606-9563","position":42,"is_corresponding":false},{"id":21377,"name":"Andrew Chess","orcid":"0000-0002-4501-8816","position":43,"is_corresponding":false},{"id":21378,"name":"Jo-fan Chien","orcid":"0000-0002-9319-6182","position":44,"is_corresponding":false},{"id":259577,"name":"Zhiyuan Chu","orcid":"0000-0002-3193-5031","position":45,"is_corresponding":false},{"id":21380,"name":"Declan Clarke","orcid":"0000-0002-6128-7485","position":46,"is_corresponding":false},{"id":1203717,"name":"Ashley Clement","orcid":null,"position":47,"is_corresponding":false},{"id":6982,"name":"Gregory M. Cooper","orcid":"0000-0001-5509-9923","position":49,"is_corresponding":false},{"id":5210,"name":"Gregory E. Crawford","orcid":"0000-0001-6106-2772","position":50,"is_corresponding":false},{"id":463255,"name":"Rujia Dai","orcid":"0000-0002-9979-3295","position":51,"is_corresponding":false},{"id":5429,"name":"Nikolaos P. Daskalakis","orcid":"0000-0003-1660-9112","position":52,"is_corresponding":false},{"id":1204,"name":"José Dávila-Velderrain","orcid":"0000-0003-0271-6267","position":53,"is_corresponding":false},{"id":21521,"name":"Amy Deep‐Soboslay","orcid":"0000-0002-7762-8942","position":54,"is_corresponding":false},{"id":21348,"name":"Chengyu Deng","orcid":"0000-0003-3595-9935","position":55,"is_corresponding":false},{"id":21385,"name":"Christopher P. DiPietro","orcid":"0009-0008-0332-2343","position":56,"is_corresponding":false},{"id":284412,"name":"Stella Dracheva","orcid":"0000-0001-5917-8688","position":57,"is_corresponding":false},{"id":21387,"name":"Shiron Drusinsky","orcid":"0000-0003-1184-8835","position":58,"is_corresponding":false},{"id":21388,"name":"Ziheng Duan","orcid":"0000-0003-4696-0042","position":59,"is_corresponding":false},{"id":21522,"name":"Duc M. Duong","orcid":"0000-0001-5880-1888","position":60,"is_corresponding":false},{"id":21390,"name":"Cagatay Dursun","orcid":"0000-0002-0897-7671","position":61,"is_corresponding":false},{"id":21523,"name":"Jonathan I. Edelstein","orcid":null,"position":63,"is_corresponding":false},{"id":21393,"name":"Prashant S. Emani","orcid":"0000-0002-3091-5231","position":64,"is_corresponding":false},{"id":284413,"name":"John F. Fullard","orcid":"0000-0001-9874-2907","position":65,"is_corresponding":false},{"id":21394,"name":"Kiki Galani","orcid":null,"position":66,"is_corresponding":false},{"id":21524,"name":"Timur R. Galeev","orcid":"0000-0002-6241-1011","position":67,"is_corresponding":false},{"id":21396,"name":"Michael J. Gandal","orcid":"0000-0001-5800-5128","position":68,"is_corresponding":false},{"id":21525,"name":"Sophia C. Gaynor","orcid":null,"position":69,"is_corresponding":false},{"id":108504,"name":"Mark Gerstein","orcid":"0000-0002-9746-3719","position":70,"is_corresponding":false},{"id":21398,"name":"Daniel H. Geschwind","orcid":"0000-0003-2896-3450","position":71,"is_corresponding":false},{"id":21399,"name":"Kiran Girdhar","orcid":"0000-0002-5622-042X","position":72,"is_corresponding":false},{"id":285221,"name":"Fernando S. Goes","orcid":"0000-0001-6262-8264","position":73,"is_corresponding":false},{"id":21400,"name":"William Greenleaf","orcid":null,"position":74,"is_corresponding":false},{"id":21401,"name":"Jennifer Grundman","orcid":"0000-0003-2266-277X","position":75,"is_corresponding":false},{"id":21402,"name":"Hanmin Guo","orcid":"0000-0001-9022-5307","position":76,"is_corresponding":false},{"id":21403,"name":"Qiuyu Guo","orcid":"0000-0001-8549-8335","position":77,"is_corresponding":false},{"id":21404,"name":"Chirag Gupta","orcid":"0000-0002-6121-7065","position":78,"is_corresponding":false},{"id":21405,"name":"Yoav Hadas","orcid":null,"position":79,"is_corresponding":false},{"id":21406,"name":"Joachim Hallmayer","orcid":"0000-0002-8520-4939","position":80,"is_corresponding":false},{"id":231293,"name":"Xikun Han","orcid":"0000-0002-3823-7308","position":81,"is_corresponding":false},{"id":1201,"name":"Vahram Haroutunian","orcid":"0000-0001-5860-2512","position":82,"is_corresponding":false},{"id":21407,"name":"Natalie Hawken","orcid":"0000-0002-0473-4373","position":83,"is_corresponding":false},{"id":634682,"name":"Chuan He","orcid":"0000-0002-6461-7515","position":84,"is_corresponding":false},{"id":1200616,"name":"Ella Henry","orcid":null,"position":85,"is_corresponding":false},{"id":21410,"name":"Marcus Ho","orcid":"0000-0002-5819-8342","position":87,"is_corresponding":false},{"id":413,"name":"Li‐Lun Ho","orcid":null,"position":88,"is_corresponding":false},{"id":1202,"name":"Gabriel E. Hoffman","orcid":"0000-0002-0957-0224","position":89,"is_corresponding":false},{"id":21526,"name":"Yi‐Ling Huang","orcid":"0009-0004-3558-4162","position":90,"is_corresponding":false},{"id":851786,"name":"Ahyeon Hwang","orcid":"0000-0002-4686-3077","position":92,"is_corresponding":false},{"id":322989,"name":"Artemis Iatrou","orcid":"0000-0001-9866-5497","position":94,"is_corresponding":false},{"id":21353,"name":"Fumitaka Inoue","orcid":"0000-0003-0657-434X","position":95,"is_corresponding":false},{"id":21415,"name":"Aarti Jajoo","orcid":null,"position":96,"is_corresponding":false},{"id":19718,"name":"Matthew Jensen","orcid":"0000-0002-5153-8543","position":97,"is_corresponding":false},{"id":21416,"name":"Lihua Jiang","orcid":"0000-0002-2895-2762","position":98,"is_corresponding":false},{"id":307991,"name":"Peng Jin","orcid":"0000-0001-6137-6659","position":99,"is_corresponding":false},{"id":21412,"name":"Louise A. Huuki-Myers","orcid":"0000-0001-5148-3602","position":0,"is_corresponding":true}],"reference_count":84,"raw_metadata":null,"created_at":"2026-07-19T01:56:50.743370Z","pmid":"38781370","pmcid":"PMC11398705","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":77.7778,"fair_a":81.25,"fair_i":40.0,"fair_r":33.3333,"fair_zscore":1.2752,"fair_rationale":{"fair_score":66.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":77.78,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The source data described in this manuscript are available from the National Institute of Mental Health (NIMH) Data Archive (https://nda.nih.gov/) (64).","grounded":true,"rationale":"A web address (https://nda.nih.gov/) is given as the place the data live, but it is not a persistent identifier scheme (DOI, Handle, ARK, URN, or repository accession). [majority verdict 'partial' (2/5 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 source data described in this manuscript are available from the National Institute of Mental Health (NIMH) Data Archive (https://nda.nih.gov/) (64).","grounded":true,"rationale":"The National Institute of Mental Health (NIMH) Data Archive is a named repository that is registered in re3data/FAIRsharing, and it is the holder of 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 source data described in this manuscript are available from the National Institute of Mental Health (NIMH) Data Archive (https://nda.nih.gov/) (64). The source data are also publicly available from the Globus endpoint 'jhpce#spatialDLPFC' and 'jhpce#DLPFC_snRNAseq' that are also listed at http://research.libd.org/globus.","grounded":true,"rationale":"The data-availability statement points to a repository (NIMH Data Archive) and provides links, fitting Colavizza category 3 (link to archived data in a public repository). [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":"For Visium, 4,866 (4.1%) spots with low library size were excluded (Fig S5), resulting in a total of 113,927 spots across 30 tissue blocks and 10 donors.","grounded":true,"rationale":"The dataset's extent (number of spots, blocks, donors) is stated in running prose, but there is no itemised inventory (section, table, or list) of files or variables. [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":1.0,"verdict":"yes","evidence":"64. Martinowich K, Maynard K, Collado-Torres L, Synapse DataSet Only T: Zintel, Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex. Synapse (2023), doi:10.7303/syn51032055.1.","grounded":true,"rationale":"The dataset identifier appears as a reference list entry (reference 64). [majority verdict 'yes' (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":81.25,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The source data are also publicly available from the Globus endpoint 'jhpce#spatialDLPFC' and 'jhpce#DLPFC_snRNAseq' that are also listed at http://research.libd.org/globus.","grounded":true,"rationale":"The text gives a route (Globus and NIMH Data Archive) with no stated precondition; the data are described as 'publicly available'.","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":"The source data are also publicly available from the Globus endpoint 'jhpce#spatialDLPFC' and 'jhpce#DLPFC_snRNAseq' that are also listed at http://research.libd.org/globus.","grounded":true,"rationale":"The paper explicitly labels the data as 'publicly available', which is a natural-language equivalent of 'open access' from the standard access-rights vocabulary.","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 paper states the data are publicly available with no gatekeeper of any kind, and no institutional or personal gatekeeper is named.","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 source data described in this manuscript are available from the National Institute of Mental Health (NIMH) Data Archive (https://nda.nih.gov/) (64).","grounded":true,"rationale":"The sentence states that the data are available now but says nothing about 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":40.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"The raw data provided through Globus include all the FASTQ files and raw image files.","grounded":true,"rationale":"FASTQ is an open, community-standard file format for sequencing data, and it is explicitly 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 (e.g., MIAME, MINSEQE, BIDS, an ontology) is named in the paper; only manuscript reporting guidelines are absent as well.","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":0.0,"verdict":"no","evidence":"All source code is publicly available through GitHub and permanently archived through Zenodo at https://github.com/LieberInstitute/spatialDLPFC (65) and https://github.com/LieberInstitute/DLPFC_snRNAseq (66).","grounded":false,"rationale":"The paper provides a repository URL for the code, which is a qualified reference to a resource other than the study's own dataset. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":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":"The paper only applies a CC BY license to the manuscript, not to the data; no license for the data is stated.","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":"Using the Visium spatial transcriptomics platform (24), we measured spatial gene expression in fresh frozen postmortem human tissue blocks","grounded":true,"rationale":"The paper names the specific platform (Visium) and other tools (10x Genomics, BayesSpace, etc.) used to produce the data. [majority verdict 'yes' (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":"No documentation object (README, data dictionary, codebook, schema) is named as travelling with the data, and no variable-definition table is present in the article.","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 given for the dataset; the data are referred to without specifying a snapshot. [majority verdict 'no' (4/5 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":0.5,"verdict":"partial","evidence":"All source code is publicly available through GitHub and permanently archived through Zenodo at https://github.com/LieberInstitute/spatialDLPFC (65) and https://github.com/LieberInstitute/DLPFC_snRNAseq (66).","grounded":false,"rationale":"A machine-resolvable locator (GitHub URL) is given for the study's own code, and it is archived via Zenodo. [downgraded to 'partial' — no verifiable quote from the paper]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"Data were generated as part of the PsychENCODE Consortium, supported by: U01DA048279, U01MH103339, U01MH103340, U01MH103346, U01MH103365, U01MH103392, U01MH116438, U01MH116441, U01MH116442, U01MH116488, U01MH116489, U01MH116492, U01MH122590, U01MH122591, U01MH122592, U01MH122849, U01MH122678, U01MH122681, U01MH116487, U01MH122509, R01MH094714, R01MH105472, R01MH105898, R01MH109677, R01MH109715, R01MH110905, R01MH110920, R01MH110921, R01MH110926, R01MH110927, R01MH110928, R01MH111721, R01MH117291, R01MH117292, R01MH117293, R21MH102791, R21MH103877, R21MH105853, R21MH105881, R21MH109956, R56MH114899, R56MH114901, R56MH114911, R01MH125516, R01MH126459, R01MH129301, R01MH126393, R01MH121521, R01MH116529, R01MH129817, R01MH117406, and P50MH106934","grounded":true,"rationale":"Multiple award/grant numbers (e.g., U01DA048279, R01MH123183) are attached to named funders (NIH, NIMH, etc.). [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":"The paper only applies a CC BY license to the manuscript, not to the data; no license for the data is stated.","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":"The source data described in this manuscript are available from the National Institute of Mental Health (NIMH) Data Archive (https://nda.nih.gov/) (64).","why":"A web address (https://nda.nih.gov/) is given as the place the data live, but it is not a persistent identifier scheme (DOI, Handle, ARK, URN, or repository accession). [majority verdict 'partial' (2/5 passes agreed)]","gain":8.33,"priority":"essential","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 source code is publicly available through GitHub and permanently archived through Zenodo at https://github.com/LieberInstitute/spatialDLPFC (65) and https://github.com/LieberInstitute/DLPFC_snRNAseq (66).","why":"A machine-resolvable locator (GitHub URL) is given for the study's own code, and it is archived via Zenodo. [downgraded to 'partial' — no verifiable quote from the paper]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No version token or date is given for the dataset; the data are referred to without specifying a snapshot. [majority verdict 'no' (4/5 passes agreed)]","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":"For Visium, 4,866 (4.1%) spots with low library size were excluded (Fig S5), resulting in a total of 113,927 spots across 30 tissue blocks and 10 donors.","why":"The dataset's extent (number of spots, blocks, donors) is stated in running prose, but there is no itemised inventory (section, table, or list) of files or variables. [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 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 (e.g., MIAME, MINSEQE, BIDS, an ontology) is named in the paper; only manuscript reporting guidelines are absent as well.","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, data dictionary, codebook, schema) is named as travelling with the data, and no variable-definition table is present in the article.","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 paper states the data are publicly available with no gatekeeper of any kind, and no institutional or personal gatekeeper is named.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All source code is publicly available through GitHub and permanently archived through Zenodo at https://github.com/LieberInstitute/spatialDLPFC (65) and https://github.com/LieberInstitute/DLPFC_snRNAseq (66).","why":"The paper provides a repository URL for the code, which is a qualified reference to a resource other than the study's own dataset. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","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 source data described in this manuscript are available from the National Institute of Mental Health (NIMH) Data Archive (https://nda.nih.gov/) (64).","why":"The sentence states that the data are available now but says nothing about 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.","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).","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).","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":"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":"2026-07-20T11:13:34.292815Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}