{"doi":"10.1002/mds.28549","title":"Accelerating Medicines Partnership: Parkinson's Disease. Genetic Resource","abstract":"BACKGROUND: Whole-genome sequencing data are available from several large studies across a variety of diseases and traits. However, massive storage and computation resources are required to use these data, and to achieve sufficient power for discoveries, harmonization of multiple cohorts is critical. OBJECTIVES: The Accelerating Medicines Partnership Parkinson's Disease program has developed a research platform for Parkinson's disease (PD) that integrates the storage and analysis of whole-genome sequencing data, RNA expression data, and clinical data, harmonized across multiple cohort studies. METHODS: The version 1 release contains whole-genome sequencing data derived from 3941 participants from 4 cohorts. Samples underwent joint genotyping by the TOPMed Freeze 9 Variant Calling Pipeline. We performed descriptive analyses of these whole-genome sequencing data using the Accelerating Medicines Partnership Parkinson's Disease platform. RESULTS: The clinical diagnosis of participants in version 1 release includes 2005 idiopathic PD patients, 963 healthy controls, 64 prodromal subjects, 62 clinically diagnosed PD subjects without evidence of dopamine deficit, and 705 participants of genetically enriched cohorts carrying PD risk-associated GBA variants or LRRK2 variants, of whom 304 were affected. We did not observe significant enrichment of pathogenic variants in the idiopathic PD group, but the polygenic risk score was higher in PD both in nongenetically enriched cohorts and genetically enriched cohorts. The population analysis showed a correlation between genetically enriched cohorts and Ashkenazi Jewish ancestry. CONCLUSIONS: We describe the genetic component of the Accelerating Medicines Partnership Parkinson's Disease platform, a solution to democratize data access and analysis for the PD research community. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article is a U.S. Government work and is in the public domain in the USA.","journal":"Movement Disorders","year":2021,"id":148263,"datarank":2.656836703720898,"base_score":4.882801922586371,"endowment":4.882801922586371,"self_citation_contribution":0.7324202883879557,"citation_network_contribution":1.9244164153329426,"self_endowment_contribution":0.7324202883879557,"citer_contribution":1.9244164153329426,"corpus_percentile":91.76916531291096,"corpus_rank":1065,"citation_count":131,"citer_count":78,"citers_with_citation_signal":56,"citers_with_endowment":56,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9105,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":41.6667,"fair_percentile":54.173035768878016,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":271542,"name":"Hampton L. Leonard","orcid":"0000-0003-2390-8110","position":1,"is_corresponding":false},{"id":271540,"name":"Mary B. Makarious","orcid":"0000-0001-7049-6281","position":2,"is_corresponding":false},{"id":564078,"name":"Matt Bookman","orcid":null,"position":3,"is_corresponding":false},{"id":564079,"name":"Barry Landin","orcid":null,"position":4,"is_corresponding":false},{"id":564080,"name":"David Vismer","orcid":null,"position":5,"is_corresponding":false},{"id":563412,"name":"Bradford Casey","orcid":"0000-0002-2623-5997","position":6,"is_corresponding":false},{"id":80301,"name":"J. Raphael Gibbs","orcid":"0000-0002-6985-0658","position":7,"is_corresponding":false},{"id":271544,"name":"Dena Hernández","orcid":"0000-0002-0188-9927","position":8,"is_corresponding":false},{"id":252390,"name":"Cornelis Blauwendraat","orcid":"0000-0001-9358-8111","position":9,"is_corresponding":false},{"id":563413,"name":"Dan Vitale","orcid":"0000-0002-0637-3671","position":10,"is_corresponding":false},{"id":433226,"name":"Yeajin Song","orcid":null,"position":11,"is_corresponding":false},{"id":563414,"name":"Dinesh Kumar","orcid":"0000-0002-6143-2507","position":12,"is_corresponding":false},{"id":241309,"name":"Clifton L. Dalgard","orcid":"0000-0003-2025-8239","position":13,"is_corresponding":false},{"id":563415,"name":"Mahdiar Sadeghi","orcid":"0000-0002-8696-0912","position":14,"is_corresponding":false},{"id":358,"name":"Xianjun Dong","orcid":"0000-0002-8052-9320","position":15,"is_corresponding":false},{"id":431564,"name":"Leonie Misquitta","orcid":null,"position":16,"is_corresponding":false},{"id":271284,"name":"Sonja W. Scholz","orcid":"0000-0002-6623-0429","position":17,"is_corresponding":false},{"id":271547,"name":"Clemens R. Scherzer","orcid":"0000-0002-0567-9193","position":18,"is_corresponding":false},{"id":130825,"name":"Mike A. Nalls","orcid":null,"position":19,"is_corresponding":false},{"id":251652,"name":"Shameek Biswas","orcid":"0000-0002-9372-1143","position":20,"is_corresponding":false},{"id":6986,"name":"Andrew Singleton","orcid":"0000-0001-5606-700X","position":21,"is_corresponding":false},{"id":564081,"name":"AMP PD Whole Genome Sequencing Working Group","orcid":null,"position":22,"is_corresponding":false},{"id":252389,"name":"Hirotaka Iwaki","orcid":"0000-0002-8982-7885","position":0,"is_corresponding":true}],"reference_count":23,"raw_metadata":null,"created_at":"2026-07-18T23:42:41.063423Z","pmid":"33960523","pmcid":"PMC8453903","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":44.4444,"fair_a":37.5,"fair_i":60.0,"fair_r":58.3333,"fair_zscore":0.2857,"fair_rationale":{"fair_score":41.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":44.44,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No persistent identifier (DOI, Handle, ARK, URN, or standard repository accession) is provided for the dataset.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The resulting CRAM files, VCFs, and jointly genotyped data (BCF, VCF, PLINK, and BigQuery format) are available through the AMP PD.","grounded":true,"rationale":"AMP PD is a project-specific platform, not a standard repository listed in re3data/FAIRsharing.","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All data processing was conducted on the Google Cloud Platform. Processing/analysis scripts were provided at the related workspaces for reference (accessible for AMP PD users). The resulting CRAM files, VCFs, and jointly genotyped data (BCF, VCF, PLINK, and BigQuery format) are available through the AMP PD.","grounded":true,"rationale":"The statement points to the AMP PD platform, which is a project-specific repository, but does not provide a direct link to a specific repository record with an accession or DOI.","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":1.0,"verdict":"yes","evidence":"TABLE 1 Whole‐genome sequenced participants","grounded":true,"rationale":"The paper includes a table (Table 1) that itemises the participants and sequencing metrics, constituting an itemised inventory of the dataset. [majority verdict 'yes' (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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No identifier for the dataset appears anywhere in the paper—neither as a reference-list entry nor in the body text—so the dataset is not cited. [majority verdict 'no' (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":37.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Processing/analysis scripts were provided at the related workspaces for reference (accessible for AMP PD users).","grounded":true,"rationale":"The availability statement includes the precondition 'accessible for AMP PD users', implying registration or approval is required to access the data.","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The resulting CRAM files, VCFs, and jointly genotyped data (BCF, VCF, PLINK, and BigQuery format) are available through the AMP PD.","grounded":true,"rationale":"The text describes the action of accessing the data through the AMP PD platform, but does not apply an explicit access-level label from the standard 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":"No gatekeeper of any kind is named; the data are simply stated as available through the AMP PD platform, with no mention of a committee, repository, or person controlling access. [majority verdict 'no' (3/5 passes agreed)]","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":null,"grounded":false,"rationale":"The paper does not state when the data become available or how long they will persist.","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"We provide various formats of data: CRAMs, BCFs, VCFs, plink binary files, and BigQuery tables.","grounded":true,"rationale":"CRAM, VCF, BCF, and PLINK are open, community-standard formats. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No data or metadata community standard (minimum information checklist, ontology, schema) is named as applying to the released data. [majority verdict 'no' (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":"We also referenced genotyping array data from GSE23636 at Gene Expression Omnibus to identify the Ashkenazi Jewish population in the study.","grounded":true,"rationale":"The paper includes an identifier (GSE23636) for a resource other than its own dataset.","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":58.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No license for the data is mentioned; the article's CC BY 4.0 license applies to the article, not the data.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"DNA samples were derived from the participants' whole‑blood specimens and sequenced using Illumina HiSeq X Ten platform at Macrogen Corp.","grounded":true,"rationale":"The paper names the specific instrument and platform (Illumina HiSeq X Ten, Macrogen) used to produce the data.","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":0.5,"verdict":"partial","evidence":"TABLE 1 Whole‐genome sequenced participants","grounded":true,"rationale":"Variable definitions (e.g., Table 1) are provided inside the article itself, not as a separate documentation object shipped with the data. [majority verdict 'partial' (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":1.0,"verdict":"yes","evidence":"The version 1 release contains whole‑genome sequencing data derived from 3941 participants from 4 cohorts.","grounded":true,"rationale":"The paper explicitly refers to 'version 1 release' as a version token for the data. [majority verdict 'yes' (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":1.0,"verdict":"yes","evidence":"https://github.com/amp-pd/amp-pd-workflows","grounded":true,"rationale":"The paper provides a GitHub URL for the workflows, which is a machine-resolvable code repository. [majority verdict 'yes' (3/5 passes agreed)]","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":"ZO1 AG000949","grounded":true,"rationale":"The paper includes specific award or grant numbers (ZO1 AG000949, IAA-XAG16001-001-00000) from the National Institutes of Health. [majority verdict 'yes' (3/5 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":"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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No persistent identifier (DOI, Handle, ARK, URN, or standard repository accession) is provided for the dataset.","gain":16.67,"priority":"essential","scored":true},{"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 for the data is mentioned; the article's CC BY 4.0 license applies to the article, not the data.","gain":16.67,"priority":"essential","scored":true},{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The resulting CRAM files, VCFs, and jointly genotyped data (BCF, VCF, PLINK, and BigQuery format) are available through the AMP PD.","why":"AMP PD is a project-specific platform, not a standard repository listed in re3data/FAIRsharing.","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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Processing/analysis scripts were provided at the related workspaces for reference (accessible for AMP PD users).","why":"The availability statement includes the precondition 'accessible for AMP PD users', implying registration or approval is required to access the data.","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 clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifier for the dataset appears anywhere in the paper—neither as a reference-list entry nor in the body text—so the dataset is not cited. [majority verdict 'no' (4/5 passes agreed)]","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 data processing was conducted on the Google Cloud Platform. Processing/analysis scripts were provided at the related workspaces for reference (accessible for AMP PD users). The resulting CRAM files, VCFs, and jointly genotyped data (BCF, VCF, PLINK, and BigQuery format) are available through the AMP PD.","why":"The statement points to the AMP PD platform, which is a project-specific repository, but does not provide a direct link to a specific repository record with an accession or DOI.","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The resulting CRAM files, VCFs, and jointly genotyped data (BCF, VCF, PLINK, and BigQuery format) are available through the AMP PD.","why":"The text describes the action of accessing the data through the AMP PD platform, but does not apply an explicit access-level label from the standard vocabulary.","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 clinical / human-subjects, describe the data with OMOP CDM, CDISC SDTM or HL7 FHIR.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No data or metadata community standard (minimum information checklist, ontology, schema) is named as applying to the released data. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"TABLE 1 Whole‐genome sequenced participants","why":"Variable definitions (e.g., Table 1) are provided inside the article itself, not as a separate documentation object shipped with the data. [majority verdict 'partial' (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 clinical / human-subjects data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No gatekeeper of any kind is named; the data are simply stated as available through the AMP PD platform, with no mention of a committee, repository, or person controlling access. [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":"no","current":0.0,"evidence":null,"why":"The paper does not state when the data become available or how long they will persist.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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.","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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 clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:00:35.910719Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}