{"doi":"10.12688/wellcomeopenres.17403.2","title":"Characteristics and outcomes of COVID-19 patients with COPD from the United States, South Korea, and Europe","abstract":"<ns4:p> <ns4:bold>Background</ns4:bold> : Characterization studies of COVID-19 patients with chronic obstructive pulmonary disease (COPD) are limited in size and scope. The aim of the study is to provide a large-scale characterization of COVID-19 patients with COPD. </ns4:p> <ns4:p> <ns4:bold>Methods</ns4:bold> : We included thirteen databases contributing data from January-June 2020 from North America (US), Europe and Asia. We defined two cohorts of patients with COVID-19 namely a ‘diagnosed’ and ‘hospitalized’ cohort. We followed patients from COVID-19 index date to 30 days or death. We performed descriptive analysis and reported the frequency of characteristics and outcomes among COPD patients with COVID-19. </ns4:p> <ns4:p> <ns4:bold>Results</ns4:bold> : The study included 934,778 patients in the diagnosed COVID-19 cohort and 177,201 in the hospitalized COVID-19 cohort. Observed COPD prevalence in the diagnosed cohort ranged from 3.8% (95%CI 3.5-4.1%) in French data to 22.7% (95%CI 22.4-23.0) in US data, and from 1.9% (95%CI 1.6-2.2) in South Korean to 44.0% (95%CI 43.1-45.0) in US data, in the hospitalized cohorts. COPD patients in the hospitalized cohort had greater comorbidity than those in the diagnosed cohort, including hypertension, heart disease, diabetes and obesity. Mortality was higher in COPD patients in the hospitalized cohort and ranged from 7.6% (95%CI 6.9-8.4) to 32.2% (95%CI 28.0-36.7) across databases. ARDS, acute renal failure, cardiac arrhythmia and sepsis were the most common outcomes among hospitalized COPD patients. </ns4:p> <ns4:p> <ns4:bold>Conclusion</ns4:bold> : COPD patients with COVID-19 have high levels of COVID-19-associated comorbidities and poor COVID-19 outcomes. Further research is required to identify patients with COPD at high risk of worse outcomes. </ns4:p>","journal":"Wellcome Open Research","year":2022,"id":294373,"datarank":0.19261657019121844,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.027824726891001992,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.027824726891001992,"corpus_percentile":34.52463835383306,"corpus_rank":8465,"citation_count":2,"citer_count":2,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9115,"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":54.1667,"fair_percentile":68.66401712014674,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":378577,"name":"Katia Verhamme","orcid":"0000-0001-8162-4904","position":1,"is_corresponding":false},{"id":32102,"name":"Anna Ostropolets","orcid":"0000-0002-0847-6682","position":2,"is_corresponding":false},{"id":225287,"name":"Kristin Kostka","orcid":"0000-0003-2595-8736","position":3,"is_corresponding":false},{"id":952691,"name":"Talita Duarte-Sales","orcid":null,"position":4,"is_corresponding":false},{"id":32121,"name":"Daniel Prieto‐Alhambra","orcid":"0000-0002-3950-6346","position":5,"is_corresponding":false},{"id":32109,"name":"Thamir M. Alshammari","orcid":"0000-0002-5630-2468","position":6,"is_corresponding":false},{"id":258088,"name":"Heba Alghoul","orcid":"0000-0001-8234-5843","position":7,"is_corresponding":false},{"id":552594,"name":"Waheed‐Ul‐Rahman Ahmed","orcid":"0000-0003-0880-0355","position":8,"is_corresponding":false},{"id":32052,"name":"Clair Blacketer","orcid":"0000-0003-2570-2124","position":9,"is_corresponding":false},{"id":11351,"name":"Scott L. DuVall","orcid":"0000-0002-4898-3865","position":10,"is_corresponding":false},{"id":32051,"name":"Lana Yin Hui Lai","orcid":"0000-0002-0485-0956","position":11,"is_corresponding":false},{"id":11398,"name":"Michael E. Matheny","orcid":"0000-0003-3217-4147","position":12,"is_corresponding":false},{"id":32103,"name":"Fredrik Nyberg","orcid":"0000-0003-0892-5668","position":13,"is_corresponding":false},{"id":32113,"name":"Jose Posada","orcid":"0000-0003-3864-0241","position":14,"is_corresponding":false},{"id":32106,"name":"Peter R. Rijnbeek","orcid":"0000-0003-0621-1979","position":15,"is_corresponding":false},{"id":588678,"name":"Henry M. Spotnitz","orcid":"0000-0003-2869-0237","position":16,"is_corresponding":false},{"id":32056,"name":"Anthony G. Sena","orcid":"0000-0001-8630-5347","position":17,"is_corresponding":false},{"id":226836,"name":"Nigam H. Shah","orcid":"0000-0001-9385-7158","position":18,"is_corresponding":false},{"id":32104,"name":"Marc A. Suchard","orcid":"0000-0001-9818-479X","position":19,"is_corresponding":false},{"id":258115,"name":"Seng Chan You","orcid":"0000-0002-5052-6399","position":20,"is_corresponding":false},{"id":2010,"name":"George Hripcsak","orcid":"0000-0003-2664-7614","position":21,"is_corresponding":false},{"id":32122,"name":"Patrick Ryan","orcid":"0000-0002-9727-2138","position":22,"is_corresponding":false},{"id":32063,"name":"Daniel R. Morales","orcid":"0000-0002-0063-8069","position":23,"is_corresponding":false},{"id":952115,"name":"David Moreno‐Martos","orcid":"0000-0002-8652-6235","position":0,"is_corresponding":true}],"reference_count":27,"raw_metadata":null,"created_at":"2026-07-19T00:31:01.450041Z","pmid":null,"pmcid":null,"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":50.0,"fair_a":81.25,"fair_i":40.0,"fair_r":33.3333,"fair_zscore":0.7804,"fair_rationale":{"fair_score":54.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All aggregate data has been made freely available for public inquiry (https://data.ohdsi.org/Covid19CharacterizationCharybdis/).","grounded":true,"rationale":"The identifier given is a web URL (https://data.ohdsi.org/...), which is not a persistent identifier scheme (no DOI, Handle, ARK, URN, or repository accession). [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All aggregate data has been made freely available for public inquiry (https://data.ohdsi.org/Covid19CharacterizationCharybdis/).","grounded":true,"rationale":"The holder named is a website (data.ohdsi.org), not a recognised repository from the list (e.g., GEO, Zenodo, Dryad) or a re3data-registered archive. [majority verdict 'partial' (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":"Underlying data Raw data from each database cannot be shared due to data privacy and governance requirements but raw data could be accessed according to the terms and conditions of each data source. The data source information including the terms and conditions for data access can be found in Table 8 . Analyses were performed locally in compliance with all applicable data privacy laws. All aggregate data has been made freely available for public inquiry (https://data.ohdsi.org/Covid19CharacterizationCharybdis/). All analytic code and result sets have been made available (https://github.com/ohdsi-studies/Covid19Characterization - Charybdis). Archived analysis code as at time of publication: https://doi.org/10.5281/zenodo.5779264. Code is available under the terms of the Apache License 2.0.","grounded":false,"rationale":"The statement points to a public repository URL for the aggregate data, which is a repository record (Colavizza category 3). [downgraded to 'partial' — no verifiable quote from the paper] [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":0.5,"verdict":"partial","evidence":"This project contains the following extended data: • Supplementary Table S1. Age and gender distribution of hospitalized COVID-19 patients with COPD. • Supplementary Table S2. Age and gender distribution of diagnosed COVID-19 patients with COPD. • Supplementary Table S3 . Prevalence of treatments in patients with COPD in the 30 days before COVID-19 diagnosis. • Supplementary Table S4 . Prevalence of outcomes in diagnosed COVID-19 patients with COPD with 95%CI. • Supplementary Figure S1 . Flow chart showing database selection. • Supplementary Figure S2 . Prevalence of age and gender among COPD patients with COVID-19 who have been diagnosed and hospitalized. • Supplementary Figure S3 . Comparison of characteristics between COPD patients with COVID-19 in the diagnosed and hospitalized cohorts by SMD. • Appendix 1 . Overview of Data Sources Screened for Eligibility and Contributing Results • Appendix 2 . Definitions and codes used to identify COVID-19 • Appendix 3 . Definitions and codes used to identify COPD patients","grounded":false,"rationale":"The paper provides an itemised list of the supplementary files (extended data) contained in the Zenodo deposit. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":0.5,"verdict":"partial","evidence":"All aggregate data has been made freely available for public inquiry (https://data.ohdsi.org/Covid19CharacterizationCharybdis/).","grounded":true,"rationale":"The dataset's identifier appears only in the body text (Data availability section), not in the reference list. [majority verdict 'partial' (3/5 passes agreed)]","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":81.25,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"All aggregate data has been made freely available for public inquiry (https://data.ohdsi.org/Covid19CharacterizationCharybdis/).","grounded":true,"rationale":"The aggregate data are stated to be freely available without any precondition.","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"All aggregate data has been made freely available for public inquiry (https://data.ohdsi.org/Covid19CharacterizationCharybdis/).","grounded":true,"rationale":"The paper labels the data as 'freely available' which is a natural-language equivalent of open access. [majority verdict 'yes' (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":"Raw data from each database cannot be shared due to data privacy and governance requirements but raw data could be accessed according to the terms and conditions of each data source.","grounded":true,"rationale":"No institutional gatekeeper (e.g., a specific repository, committee, or agreement) is named for the sensitive raw data; only a vague reference to each data source's terms is given.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"All aggregate data has been made freely available for public inquiry (https://data.ohdsi.org/Covid19CharacterizationCharybdis/).","grounded":true,"rationale":"The paper states when the data are available (freely available now) but makes no commitment to how long they will persist. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":40.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file format is named for the released aggregate data.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"All data for were standardized to the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) 8,9.","grounded":true,"rationale":"The paper names the OMOP Common Data Model and SNOMED CT codes, both of which are community data/metadata standards registered in FAIRsharing.","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 persistent identifier for an external resource (beyond routine references) is provided for the data's dependencies. [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":33.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Data are available under the terms of the Creative Commons Attribution 4.0 International Public License (Attribution 4.0 International).","grounded":false,"rationale":"The paper names an open standard license (CC BY 4.0) for the data. [downgraded to 'partial' — no verifiable quote from the paper]","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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not name specific instruments, kits, or software used to produce the data (only generic analysis methods). [majority verdict 'no' (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":"Appendix 2. Definitions and codes used to identify COVID-19","grounded":false,"rationale":"The variable/code definitions are provided inside the article (appendices), not as a separate documentation object shipped with the data. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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":null,"grounded":false,"rationale":"No version token or date is stated for the dataset itself; the code archive has a version, but the data do not. [majority verdict 'no' (3/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"All analytic code and result sets have been made available (https://github.com/ohdsi-studies/Covid19Characterization - Charybdis). Archived analysis code as at time of publication: https://doi.org/10.5281/zenodo.5779264.","grounded":false,"rationale":"A machine-resolvable locator (GitHub URL and Zenodo DOI) is provided for the code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 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":"The European Health Data & Evidence Network has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 806968.","grounded":true,"rationale":"The paper gives specific grant/agreement numbers for 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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All aggregate data has been made freely available for public inquiry (https://data.ohdsi.org/Covid19CharacterizationCharybdis/).","why":"The identifier given is a web URL (https://data.ohdsi.org/...), which is not a persistent identifier scheme (no DOI, Handle, ARK, URN, or repository accession). [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"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":"All aggregate data has been made freely available for public inquiry (https://data.ohdsi.org/Covid19CharacterizationCharybdis/).","why":"The holder named is a website (data.ohdsi.org), not a recognised repository from the list (e.g., GEO, Zenodo, Dryad) or a re3data-registered archive. [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"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":"partial","current":0.5,"evidence":"Data are available under the terms of the Creative Commons Attribution 4.0 International Public License (Attribution 4.0 International).","why":"The paper names an open standard license (CC BY 4.0) for the data. [downgraded to 'partial' — no verifiable quote from the paper]","gain":8.33,"priority":"essential","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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format is named for the released aggregate data.","gain":8.33,"priority":"important","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":"partial","current":0.5,"evidence":"All aggregate data has been made freely available for public inquiry (https://data.ohdsi.org/Covid19CharacterizationCharybdis/).","why":"The dataset's identifier appears only in the body text (Data availability section), not in the reference list. [majority verdict 'partial' (3/5 passes agreed)]","gain":4.17,"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":"All analytic code and result sets have been made available (https://github.com/ohdsi-studies/Covid19Characterization - Charybdis). Archived analysis code as at time of publication: https://doi.org/10.5281/zenodo.5779264.","why":"A machine-resolvable locator (GitHub URL and Zenodo DOI) is provided for the code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 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":null,"why":"No version token or date is stated for the dataset itself; the code archive has a version, but the data do not. [majority verdict 'no' (3/5 passes agreed)]","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":"Underlying data Raw data from each database cannot be shared due to data privacy and governance requirements but raw data could be accessed according to the terms and conditions of each data source. The data source information including the terms and conditions for data access can be found in Table 8 . Analyses were performed locally in compliance with all applicable data privacy laws. All aggregate data has been made freely available for public inquiry (https://data.ohdsi.org/Covid19CharacterizationCharybdis/). All analytic code and result sets have been made available (https://github.com/ohdsi-studies/Covid19Characterization - Charybdis). Archived analysis code as at time of publication: https://doi.org/10.5281/zenodo.5779264. Code is available under the terms of the Apache License 2.0.","why":"The statement points to a public repository URL for the aggregate data, which is a repository record (Colavizza category 3). [downgraded to 'partial' — no verifiable quote from the paper] [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":"partial","current":0.5,"evidence":"This project contains the following extended data: • Supplementary Table S1. Age and gender distribution of hospitalized COVID-19 patients with COPD. • Supplementary Table S2. Age and gender distribution of diagnosed COVID-19 patients with COPD. • Supplementary Table S3 . Prevalence of treatments in patients with COPD in the 30 days before COVID-19 diagnosis. • Supplementary Table S4 . Prevalence of outcomes in diagnosed COVID-19 patients with COPD with 95%CI. • Supplementary Figure S1 . Flow chart showing database selection. • Supplementary Figure S2 . Prevalence of age and gender among COPD patients with COVID-19 who have been diagnosed and hospitalized. • Supplementary Figure S3 . Comparison of characteristics between COPD patients with COVID-19 in the diagnosed and hospitalized cohorts by SMD. • Appendix 1 . Overview of Data Sources Screened for Eligibility and Contributing Results • Appendix 2 . Definitions and codes used to identify COVID-19 • Appendix 3 . Definitions and codes used to identify COPD patients","why":"The paper provides an itemised list of the supplementary files (extended data) contained in the Zenodo deposit. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","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":"no","current":0.0,"evidence":null,"why":"The paper does not name specific instruments, kits, or software used to produce the data (only generic analysis methods). [majority verdict 'no' (2/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"Appendix 2. Definitions and codes used to identify COVID-19","why":"The variable/code definitions are provided inside the article (appendices), not as a separate documentation object shipped with the data. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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":"Raw data from each database cannot be shared due to data privacy and governance requirements but raw data could be accessed according to the terms and conditions of each data source.","why":"No institutional gatekeeper (e.g., a specific repository, committee, or agreement) is named for the sensitive raw data; only a vague reference to each data source's terms is given.","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 persistent identifier for an external resource (beyond routine references) is provided for the data's dependencies. [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":"partial","current":0.5,"evidence":"All aggregate data has been made freely available for public inquiry (https://data.ohdsi.org/Covid19CharacterizationCharybdis/).","why":"The paper states when the data are available (freely available now) but makes no commitment to how long they will persist. [majority verdict 'partial' (4/5 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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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).","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.","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.","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":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T13:20:44.682161Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}