{"doi":"10.1093/nar/gkac1010","title":"The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource","abstract":"The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare and industry. The Catalog contains variant-trait associations and supporting metadata for >45 000 published GWAS across >5000 human traits, and >40 000 full P-value summary statistics datasets. Content is curated from publications or acquired via author submission of prepublication summary statistics through a new submission portal and validation tool. GWAS data volume has vastly increased in recent years. We have updated our software to meet this scaling challenge and to enable rapid release of submitted summary statistics. The scope of the repository has expanded to include additional data types of high interest to the community, including sequencing-based GWAS, gene-based analyses and copy number variation analyses. Community outreach has increased the number of shared datasets from under-represented traits, e.g. cancer, and we continue to contribute to awareness of the lack of population diversity in GWAS. Interoperability of the Catalog has been enhanced through links to other resources including the Polygenic Score Catalog and the International Mouse Phenotyping Consortium, refinements to GWAS trait annotation, and the development of a standard format for GWAS data.","journal":"Nucleic Acids Research","year":2022,"id":231550,"datarank":5.2017222981447535,"base_score":7.469654172932128,"endowment":7.469654172932128,"self_citation_contribution":1.1204481259398194,"citation_network_contribution":4.081274172204934,"self_endowment_contribution":1.1204481259398194,"citer_contribution":4.081274172204934,"corpus_percentile":95.97741161909182,"corpus_rank":521,"citation_count":1753,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9516,"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":66.6667,"fair_percentile":86.48731274839498,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":838679,"name":"Abayomi Mosaku","orcid":"0000-0002-5783-9662","position":1,"is_corresponding":false},{"id":838680,"name":"Ala Abid","orcid":"0000-0002-6633-6434","position":2,"is_corresponding":false},{"id":88395,"name":"Annalisa Buniello","orcid":"0000-0002-4623-8642","position":3,"is_corresponding":false},{"id":62189,"name":"María Cerezo","orcid":"0000-0003-3073-1130","position":4,"is_corresponding":false},{"id":61879,"name":"Laurent Gil","orcid":"0000-0002-9475-4502","position":5,"is_corresponding":false},{"id":27575,"name":"Tudor Groza","orcid":"0000-0003-2267-8333","position":6,"is_corresponding":false},{"id":838681,"name":"Osman Güneş","orcid":"0000-0002-4987-6981","position":7,"is_corresponding":false},{"id":88409,"name":"Peggy Hall","orcid":null,"position":8,"is_corresponding":false},{"id":88398,"name":"James Hayhurst","orcid":"0000-0002-7460-403X","position":9,"is_corresponding":false},{"id":838682,"name":"Arwa Ibrahim","orcid":"0000-0001-6757-4744","position":10,"is_corresponding":false},{"id":838683,"name":"Yue Ji","orcid":"0000-0001-9844-7297","position":11,"is_corresponding":false},{"id":838684,"name":"Sajo John","orcid":"0000-0003-3029-0857","position":12,"is_corresponding":false},{"id":667589,"name":"Elizabeth Lewis","orcid":"0000-0002-1142-1359","position":13,"is_corresponding":false},{"id":88396,"name":"Jacqueline A. L. MacArthur","orcid":"0000-0002-3550-9769","position":14,"is_corresponding":false},{"id":88400,"name":"Aoife McMahon","orcid":"0000-0003-0978-0309","position":15,"is_corresponding":false},{"id":95747,"name":"David Osumi-Sutherland","orcid":"0000-0002-7073-9172","position":16,"is_corresponding":false},{"id":31263,"name":"Kalliope Panoutsopoulou","orcid":"0000-0002-5460-8025","position":17,"is_corresponding":false},{"id":95748,"name":"Zoë May Pendlington","orcid":"0000-0002-4071-8397","position":18,"is_corresponding":false},{"id":838685,"name":"Santhi Ramachandran","orcid":"0000-0002-2376-0614","position":19,"is_corresponding":false},{"id":95757,"name":"Ray Stefancsik","orcid":"0000-0001-8314-2140","position":20,"is_corresponding":false},{"id":838686,"name":"Jonathan Stewart","orcid":"0000-0003-3901-9422","position":21,"is_corresponding":false},{"id":5932,"name":"Patricia L. Whetzel","orcid":"0000-0002-3458-4839","position":22,"is_corresponding":false},{"id":838687,"name":"Robert Wilson","orcid":"0000-0002-9407-5526","position":23,"is_corresponding":false},{"id":275115,"name":"Lucia A. Hindorff","orcid":"0000-0002-4414-3236","position":24,"is_corresponding":false},{"id":35062,"name":" Fiona Cunningham","orcid":"0000-0002-7445-2419","position":25,"is_corresponding":false},{"id":551616,"name":"Samuel A. Lambert","orcid":"0000-0001-8222-008X","position":26,"is_corresponding":false},{"id":33743,"name":"Michael Inouye","orcid":"0000-0001-9413-6520","position":27,"is_corresponding":false},{"id":2833,"name":"Helen Parkinson","orcid":"0000-0003-3035-4195","position":28,"is_corresponding":false},{"id":88397,"name":"Laura W. Harris","orcid":"0000-0003-4312-7223","position":29,"is_corresponding":false},{"id":88403,"name":"Elliot Sollis","orcid":"0000-0003-1322-388X","position":0,"is_corresponding":true}],"reference_count":24,"raw_metadata":null,"created_at":"2026-07-19T00:20:51.245255Z","pmid":"36350656","pmcid":"PMC9825413","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":33.3333,"fair_a":62.5,"fair_i":40.0,"fair_r":66.6667,"fair_zscore":1.2752,"fair_rationale":{"fair_score":66.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":33.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"The NHGRI-EBI GWAS Catalog ( www.ebi.ac.uk/gwas ) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200,000 users per year from academic research, healthcare and industry.","grounded":false,"rationale":"The paper provides a URL for the Catalog, which is not a persistent identifier scheme (DOI, Handle, ARK, URN, or repository accession). [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The NHGRI-EBI GWAS Catalog ( www.ebi.ac.uk/gwas ) is the largest and most complete publicly available resource of Findable, Accessible, Interoperable and Reusable (FAIR) GWAS data.","grounded":true,"rationale":"The GWAS Catalog is a named repository (EMBL-EBI resource, listed in re3data). [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Curated data are available from the query interface ( https://www.ebi.ac.uk/gwas/ ) and download files from https://www.ebi.ac.uk/gwas/downloads .","grounded":true,"rationale":"The statement points to the repository's homepage but not to a specific record with an accession or DOI. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"The Catalog contains variant-trait associations and supporting metadata for >45,000 published GWAS across >5,000 human traits, and >40,000 full P-value summary statistics datasets.","grounded":false,"rationale":"The dataset's content is described in running prose, not in an itemised inventory (section, table, or list). [downgraded to 'no' — no verifiable quote from the paper]","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 in the text, either in the body or in the reference list. [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":62.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Curated data are available from the query interface ( https://www.ebi.ac.uk/gwas/ ) and download files from https://www.ebi.ac.uk/gwas/downloads .","grounded":true,"rationale":"The text gives a direct route to the data with no stated precondition. [majority verdict 'yes' (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":0.5,"verdict":"partial","evidence":"GWAS summary statistics submitted after March 2021 are made available under CC0 terms ( https://creativecommons.org/publicdomain/zero/1.0/ ).","grounded":false,"rationale":"The paper explicitly labels the access level using the CC0 licence, which is a standard open-access label. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are summary statistics and not sensitive human-subject data; no 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No sentence states how long the data will remain available or any persistence commitment. [majority verdict 'no' (3/5 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":0.5,"verdict":"partial","evidence":"Summary statistics files are transferred to the GWAS Catalog using Globus. To ensure data completeness, interoperability and reusability, summary statistics are required to conform to the GWAS Catalog's standard format, which includes a consistent .tsv file format, and mandatory and recommended fields.","grounded":false,"rationale":"The paper names .tsv, an open, community-standard format. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":0.5,"verdict":"partial","evidence":"Traits are described in a flexible free text field reflecting author language and study design, and annotated using terms from the Experimental Factor Ontology (EFO) to enable searchability and interoperability.","grounded":false,"rationale":"The paper names the Experimental Factor Ontology (EFO), a community standard ontology. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No identifier for an external resource is provided in a sentence that predicates a reference to it from this study's data. [majority verdict 'no' (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":66.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"GWAS summary statistics submitted after March 2021 are made available under CC0 terms ( https://creativecommons.org/publicdomain/zero/1.0/ )","grounded":true,"rationale":"CC0 is an open standard licence. [majority verdict 'yes' (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":0.5,"verdict":"partial","evidence":"Data is acquired through a combination of deep learning methods to identify publications, curation of publications by expert scientists, and direct data submission by authors.","grounded":true,"rationale":"The methods are described in generic terms without naming specific instruments or software versions. [majority verdict 'partial' (2/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No documentation object (README, codebook) is named to accompany the data, and no variable-definition table is provided in the article. [majority verdict 'no' (4/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"As of July 2022, the GWAS Catalog contains ~400,000 curated SNP-trait associations from >45,000 individual GWAS in ~6000 publications.","grounded":false,"rationale":"A date pins the snapshot, but no version token is given. [downgraded to 'no' — no verifiable quote from the paper]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"The GWAS Catalog is an open-source project and code is available in the project's github repository ( https://github.com/EBISPOT/goci ).","grounded":true,"rationale":"A code-forge URL is provided for the study's own code. [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":"National Human Genome Research Institute of the National Institutes of Health [U41-HG007823, ‘Phenomics First’ RM1HG010860];","grounded":true,"rationale":"Award numbers are given for the funding. [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":"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":"no","current":0.0,"evidence":"The NHGRI-EBI GWAS Catalog ( www.ebi.ac.uk/gwas ) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200,000 users per year from academic research, healthcare and industry.","why":"The paper provides a URL for the Catalog, which is not a persistent identifier scheme (DOI, Handle, ARK, URN, or repository accession). [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifier for the dataset appears in the text, either in the body or in the reference list. [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 genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Summary statistics files are transferred to the GWAS Catalog using Globus. To ensure data completeness, interoperability and reusability, summary statistics are required to conform to the GWAS Catalog's standard format, which includes a consistent .tsv file format, and mandatory and recommended fields.","why":"The paper names .tsv, an open, community-standard format. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"As of July 2022, the GWAS Catalog contains ~400,000 curated SNP-trait associations from >45,000 individual GWAS in ~6000 publications.","why":"A date pins the snapshot, but no version token is given. [downgraded to 'no' — no verifiable quote from the paper]","gain":4.17,"priority":"useful","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":"Curated data are available from the query interface ( https://www.ebi.ac.uk/gwas/ ) and download files from https://www.ebi.ac.uk/gwas/downloads .","why":"The statement points to the repository's homepage but not to a specific record with an accession or DOI. [majority verdict 'partial' (4/5 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":"no","current":0.0,"evidence":"The Catalog contains variant-trait associations and supporting metadata for >45,000 published GWAS across >5,000 human traits, and >40,000 full P-value summary statistics datasets.","why":"The dataset's content is described in running prose, not in an itemised inventory (section, table, or list). [downgraded to 'no' — no verifiable quote from the paper]","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":"GWAS summary statistics submitted after March 2021 are made available under CC0 terms ( https://creativecommons.org/publicdomain/zero/1.0/ ).","why":"The paper explicitly labels the access level using the CC0 licence, which is a standard open-access label. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Traits are described in a flexible free text field reflecting author language and study design, and annotated using terms from the Experimental Factor Ontology (EFO) to enable searchability and interoperability.","why":"The paper names the Experimental Factor Ontology (EFO), a community standard ontology. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Data is acquired through a combination of deep learning methods to identify publications, curation of publications by expert scientists, and direct data submission by authors.","why":"The methods are described in generic terms without naming specific instruments or software versions. [majority verdict 'partial' (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 documentation object (README, codebook) is named to accompany the data, and no variable-definition table is provided in the article. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are summary statistics and not sensitive human-subject data; no 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":null,"why":"No identifier for an external resource is provided in a sentence that predicates a reference to it from this study's data. [majority verdict 'no' (4/5 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":"No sentence states how long the data will remain available or any persistence commitment. [majority verdict 'no' (3/5 passes agreed)]","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","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.","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."],"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":"2026-07-20T10:45:53.218715Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}