{"doi":"10.1093/nar/gky1120","title":"The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019","abstract":"The GWAS Catalog delivers a high-quality curated collection of all published genome-wide association studies enabling investigations to identify causal variants, understand disease mechanisms, and establish targets for novel therapies. The scope of the Catalog has also expanded to targeted and exome arrays with 1000 new associations added for these technologies. As of September 2018, the Catalog contains 5687 GWAS comprising 71673 variant-trait associations from 3567 publications. New content includes 284 full P-value summary statistics datasets for genome-wide and new targeted array studies, representing 6 × 109 individual variant-trait statistics. In the last 12 months, the Catalog's user interface was accessed by ∼90000 unique users who viewed >1 million pages. We have improved data access with the release of a new RESTful API to support high-throughput programmatic access, an improved web interface and a new summary statistics database. Summary statistics provision is supported by a new format proposed as a community standard for summary statistics data representation. This format was derived from our experience in standardizing heterogeneous submissions, mapping formats and in harmonizing content. Availability: https://www.ebi.ac.uk/gwas/.","journal":"Nucleic Acids Research","year":2018,"id":10781,"datarank":9.634739967413056,"base_score":8.443115988019922,"endowment":8.443115988019922,"self_citation_contribution":1.2664673982029886,"citation_network_contribution":8.368272569210067,"self_endowment_contribution":1.2664673982029886,"citer_contribution":8.368272569210067,"corpus_percentile":98.61530130734123,"corpus_rank":180,"citation_count":4642,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9466,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2018-11-16","fair_score":43.75,"fair_percentile":58.6365025985937,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":88396,"name":"Jacqueline A. L. MacArthur","orcid":"0000-0002-3550-9769","position":1,"is_corresponding":false},{"id":62058,"name":"Uday S. Evani","orcid":"0009-0002-2057-4514","position":2,"is_corresponding":false},{"id":88397,"name":"Laura W. Harris","orcid":"0000-0003-4312-7223","position":3,"is_corresponding":false},{"id":88398,"name":"James Hayhurst","orcid":"0000-0002-7460-403X","position":4,"is_corresponding":false},{"id":88399,"name":"Cinzia Malangone","orcid":null,"position":5,"is_corresponding":false},{"id":88400,"name":"Aoife McMahon","orcid":"0000-0003-0978-0309","position":6,"is_corresponding":false},{"id":88401,"name":"Joannella Morales","orcid":"0000-0002-8121-9797","position":7,"is_corresponding":false},{"id":88402,"name":"Edward Mountjoy","orcid":"0000-0002-0626-1821","position":8,"is_corresponding":false},{"id":88403,"name":"Elliot Sollis","orcid":"0000-0003-1322-388X","position":9,"is_corresponding":false},{"id":88404,"name":"Daniel Suveges","orcid":null,"position":10,"is_corresponding":false},{"id":88405,"name":"Olga Vrousgou","orcid":"0000-0003-4917-4784","position":11,"is_corresponding":false},{"id":5932,"name":"Patricia L. Whetzel","orcid":"0000-0002-3458-4839","position":12,"is_corresponding":false},{"id":88406,"name":"Ridwan Amode","orcid":null,"position":13,"is_corresponding":false},{"id":88407,"name":"Jose A Guillen","orcid":null,"position":14,"is_corresponding":false},{"id":88408,"name":"Harpreet S Riat","orcid":null,"position":15,"is_corresponding":false},{"id":29379,"name":"Stephen J. Trevanion","orcid":"0000-0002-4862-3333","position":16,"is_corresponding":false},{"id":88409,"name":"Peggy Hall","orcid":null,"position":17,"is_corresponding":false},{"id":58372,"name":"Heather A. Junkins","orcid":null,"position":18,"is_corresponding":false},{"id":20075,"name":"David B. Jaffe","orcid":"0000-0001-8739-568X","position":19,"is_corresponding":false},{"id":2487,"name":"Tony Burdett","orcid":"0000-0002-2513-5396","position":20,"is_corresponding":false},{"id":21886,"name":"Andrew T. Hattersley","orcid":"0000-0001-5620-473X","position":21,"is_corresponding":false},{"id":35062,"name":" Fiona Cunningham","orcid":"0000-0002-7445-2419","position":22,"is_corresponding":false},{"id":2833,"name":"Helen Parkinson","orcid":"0000-0003-3035-4195","position":23,"is_corresponding":false},{"id":62189,"name":"María Cerezo","orcid":"0000-0003-3073-1130","position":24,"is_corresponding":false},{"id":88410,"name":"Claudio Malangone","orcid":"0000-0003-1639-8589","position":25,"is_corresponding":false},{"id":88411,"name":"Dániel Süveges","orcid":"0000-0003-4133-0447","position":26,"is_corresponding":false},{"id":88412,"name":"José Ángel Guillén","orcid":"0000-0003-4220-2471","position":27,"is_corresponding":false},{"id":88413,"name":"Harpreet Singh Riat","orcid":null,"position":28,"is_corresponding":false},{"id":88395,"name":"Annalisa Buniello","orcid":"0000-0002-4623-8642","position":0,"is_corresponding":true}],"reference_count":35,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"30445434","pmcid":"PMC6323933","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":44.4444,"fair_a":37.5,"fair_i":80.0,"fair_r":29.1667,"fair_zscore":0.3681,"fair_rationale":{"fair_score":43.75,"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":"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":false,"rationale":"The paper provides a URL for the data, which is a web address, not a persistent-identifier scheme such as a DOI or Handle. [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 GWAS Catalog delivers a high-quality curated collection of all published genome-wide association studies","grounded":true,"rationale":"The GWAS Catalog is named as the repository; it is a curated public archive listed in re3data. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"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":false,"rationale":"The data-availability statement points to a repository (the GWAS Catalog) with persistent URLs, satisfying the condition for a repository record. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"As of September 2018, the Catalog contains 5687 GWAS comprising 71673 variant-trait associations from 3567 publications.","grounded":true,"rationale":"The paper describes the dataset's content and size in a single sentence, not in an itemised inventory such as a table or list.","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":"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":false,"rationale":"The dataset identifier (the URL) appears only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [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":"The GWAS Catalog is a publicly available resource of published human GWAS.","grounded":false,"rationale":"The paper states the data are publicly available without any precondition, meeting the definition of unconditional access. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The GWAS Catalog is a publicly available resource of published human GWAS.","grounded":false,"rationale":"The paper explicitly labels the data as 'publicly available', which is a natural-language equivalent of the 'open access' access-level label. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not name any gatekeeper for the Catalog's own data, which are aggregate summary statistics and are openly available.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not state any persistence commitment or availability timing for the data beyond the current release.","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":80.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"a GWAS Catalog summary statistics datastore, based on the HDF5 library format","grounded":true,"rationale":"The paper names HDF5, an open, community-standard file format. [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":0.5,"verdict":"partial","evidence":"Traits in the Catalog are represented using the Experimental Factor Ontology (EFO, (22)).","grounded":false,"rationale":"The paper names the Experimental Factor Ontology (EFO), a community standard ontology registered in FAIRsharing. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"UK Biobank ( http://www.ukbiobank.ac.uk/ )","grounded":true,"rationale":"The paper provides a URL identifier for the UK Biobank, a resource used by the study that is not the dataset itself. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":29.17,"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 does not state any licence for the Catalog data; the CC BY licence applies only to the article.","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":"Manual curation of each publication by expert scientists ensures that the Catalog provides accurate and structured metadata","grounded":true,"rationale":"The production method is described in generic terms without naming specific instruments, kits, 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":"Our standard format contains a minimal set of requirements that are included in the outputs from the most common GWAS analysis programs (such as PLINK, (29) and additional optional columns.","grounded":false,"rationale":"The paper describes the data format in the text but does not name a documentation object shipped with the data. [downgraded to 'no' — no verifiable quote from the paper]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"As of September 2018, the Catalog contains 5687 GWAS comprising 71673 variant-trait associations from 3567 publications.","grounded":true,"rationale":"The paper uses a date (September 2018) to indicate the snapshot, but no version token is given.","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":"The GWAS Catalog is an open source project and code is available in the project's github repository (https://github.com/EBISPOT/goci).","grounded":false,"rationale":"The paper provides a machine-resolvable GitHub URL for the project code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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]; Open Targets [OTAR034, OTAR2045]","grounded":true,"rationale":"The paper includes specific award numbers for the funding.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"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":"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 paper provides a URL for the data, which is a web address, not a persistent-identifier scheme such as a DOI or Handle. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","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":"The paper does not state any licence for the Catalog data; the CC BY licence applies only to the article.","gain":16.67,"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 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 GWAS Catalog is a publicly available resource of published human GWAS.","why":"The paper states the data are publicly available without any precondition, meeting the definition of unconditional access. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"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 dataset identifier (the URL) appears only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":8.33,"priority":"important","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":"The GWAS Catalog is an open source project and code is available in the project's github repository (https://github.com/EBISPOT/goci).","why":"The paper provides a machine-resolvable GitHub URL for the project code. [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":"partial","current":0.5,"evidence":"As of September 2018, the Catalog contains 5687 GWAS comprising 71673 variant-trait associations from 3567 publications.","why":"The paper uses a date (September 2018) to indicate the snapshot, but no version token is given.","gain":2.08,"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 data-availability statement points to a repository (the GWAS Catalog) with persistent URLs, satisfying the condition for a repository record. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"As of September 2018, the Catalog contains 5687 GWAS comprising 71673 variant-trait associations from 3567 publications.","why":"The paper describes the dataset's content and size in a single sentence, not in an itemised inventory such as a table or list.","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 GWAS Catalog is a publicly available resource of published human GWAS.","why":"The paper explicitly labels the data as 'publicly available', which is a natural-language equivalent of the 'open access' access-level label. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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 in the Catalog are represented using the Experimental Factor Ontology (EFO, (22)).","why":"The paper names the Experimental Factor Ontology (EFO), a community standard ontology registered in FAIRsharing. [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":"Manual curation of each publication by expert scientists ensures that the Catalog provides accurate and structured metadata","why":"The production method is described in generic terms without naming specific instruments, kits, 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":"Our standard format contains a minimal set of requirements that are included in the outputs from the most common GWAS analysis programs (such as PLINK, (29) and additional optional columns.","why":"The paper describes the data format in the text but does not name a documentation object shipped with the data. [downgraded to 'no' — no verifiable quote from the paper]","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 does not name any gatekeeper for the Catalog's own data, which are aggregate summary statistics and are openly available.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not state any persistence commitment or availability timing for the data beyond the current release.","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).","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.","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 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.","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)."],"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":"2026-07-20T10:44:34.931346Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}