{"doi":"10.1093/ofid/ofaf572","title":"Accelerating Cough-Based Algorithms for Pulmonary Tuberculosis Screening: Results From the CODA TB DREAM Challenge","abstract":"Background: Open-access data challenges can accelerate innovation in artificial intelligence-based tools. In the Cough Diagnostic Algorithm for Tuberculosis (CODA TB) DREAM Challenge, we developed and independently validated cough sound-based artificial intelligence algorithms for tuberculosis screening. Methods: We included data from 2143 adults with ≥2 weeks of cough from outpatient clinics in India, Madagascar, the Philippines, South Africa, Tanzania, Uganda, and Vietnam. A standard tuberculosis evaluation was completed, and ≥3 solicited coughs were recorded using a smartphone. We invited teams to develop models using training data to classify microbiologically confirmed tuberculosis disease using (1) cough sound features only and/or (2) cough sound features with routinely available clinical data. After 4 months, they submitted the algorithms for independent test set validation. Models were ranked by area under the receiver operating characteristic curve (AUROC) and partial AUROC (pAUROC) to achieve at least 80% sensitivity and 60% specificity. Results: Eleven cough models and 6 cough-plus-clinical models were submitted. AUROCs for cough models ranged from 0.69 to 0.74, and the highest performing model achieved 55.5% specificity (95% confidence interval, 47.7%-64.2%) at 80% sensitivity. The addition of clinical data improved AUROCs (range, 0.78-0.83); 5 of the 6 models reached the target pAUROC, and the highest performing model had 73.8% specificity (95% confidence interval, 60.8%-80.0%) at 80% sensitivity. The AUROC varied by country and was higher among male and human immunodeficiency virus-negative individuals. Conclusions: In a short period, an open-access data challenge facilitated the development of new cough-based tuberculosis algorithms and demonstrated potential as a tuberculosis screening tool.","journal":"Open Forum Infectious Diseases","year":2025,"id":542343,"datarank":0.16479184330021646,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.0,"corpus_percentile":29.844511487584125,"corpus_rank":8690,"citation_count":2,"citer_count":1,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8892,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":45.8333,"fair_percentile":59.49250993579945,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":27470,"name":"Solveig K. Sieberts","orcid":"0000-0003-1033-0954","position":1,"is_corresponding":false},{"id":882534,"name":"Mihaja Raberahona","orcid":"0000-0001-8857-5834","position":2,"is_corresponding":false},{"id":924551,"name":"Sophie Huddart","orcid":"0000-0001-6425-3371","position":3,"is_corresponding":false},{"id":13888,"name":"Larsson Omberg","orcid":"0000-0002-4719-9120","position":4,"is_corresponding":false},{"id":1325958,"name":"Rivo Andry Rakotoarivelo","orcid":"0000-0003-3438-8624","position":5,"is_corresponding":false},{"id":1325957,"name":"Issa N. Lyimo","orcid":"0000-0001-5804-7352","position":6,"is_corresponding":false},{"id":534882,"name":"Omar Lweno","orcid":"0000-0003-4657-0124","position":7,"is_corresponding":false},{"id":497200,"name":"Devasahayam Jesudas Christopher","orcid":"0000-0002-9405-8494","position":8,"is_corresponding":false},{"id":346879,"name":"Nguyen Viet Nhung","orcid":"0000-0002-5447-133X","position":9,"is_corresponding":false},{"id":363347,"name":"William Worodria","orcid":"0000-0002-8531-5567","position":10,"is_corresponding":false},{"id":799543,"name":"Charles Yu","orcid":null,"position":11,"is_corresponding":false},{"id":89840,"name":"Jhih-Yu Chen","orcid":"0000-0003-1652-8566","position":12,"is_corresponding":false},{"id":89838,"name":"Sz-Hau Chen","orcid":null,"position":13,"is_corresponding":false},{"id":89879,"name":"Tsai‐Min Chen","orcid":"0000-0002-1143-0677","position":14,"is_corresponding":false},{"id":89835,"name":"Chih-Han Huang","orcid":"0000-0001-7339-1194","position":15,"is_corresponding":false},{"id":89841,"name":"Kuei-Lin Huang","orcid":null,"position":16,"is_corresponding":false},{"id":1431917,"name":"Filip Mulier","orcid":null,"position":17,"is_corresponding":false},{"id":1431416,"name":"Daniel Rafter","orcid":"0000-0002-5608-7382","position":18,"is_corresponding":false},{"id":89880,"name":"Edward S.C. Shih","orcid":"0000-0002-8175-0393","position":19,"is_corresponding":false},{"id":1431417,"name":"Yu Tsao","orcid":"0000-0001-6956-0418","position":20,"is_corresponding":false},{"id":1431418,"name":"Hsuan-Kai Wang","orcid":"0000-0002-2157-0091","position":21,"is_corresponding":false},{"id":89881,"name":"Chih‐Hsun Wu","orcid":"0000-0003-4613-5915","position":22,"is_corresponding":false},{"id":925753,"name":"Christine Bachman","orcid":"0000-0002-8143-2782","position":23,"is_corresponding":false},{"id":1326494,"name":"Stephen Burkot","orcid":null,"position":24,"is_corresponding":false},{"id":983435,"name":"Puneet Dewan","orcid":"0000-0001-5798-300X","position":25,"is_corresponding":false},{"id":1326495,"name":"Sourabh Kulhare","orcid":null,"position":26,"is_corresponding":false},{"id":1167523,"name":"Peter M. Small","orcid":"0000-0001-5403-8985","position":27,"is_corresponding":false},{"id":1325970,"name":"Vijay Yadav","orcid":"0000-0003-2801-9005","position":28,"is_corresponding":false},{"id":1207271,"name":"Simon Grandjean Lapierre","orcid":"0000-0003-3646-1573","position":29,"is_corresponding":false},{"id":244855,"name":"Grant Theron","orcid":"0000-0002-9216-2415","position":30,"is_corresponding":false},{"id":315466,"name":"Adithya Cattamanchi","orcid":"0000-0002-6553-2601","position":31,"is_corresponding":false},{"id":1431419,"name":"Gautam Ahuja","orcid":"0000-0003-1645-0068","position":32,"is_corresponding":false},{"id":1431918,"name":"Shalini Balodi","orcid":null,"position":33,"is_corresponding":false},{"id":1431919,"name":"Diya Khurdiya","orcid":null,"position":34,"is_corresponding":false},{"id":557039,"name":"Rintu Kutum","orcid":"0000-0001-8667-6199","position":35,"is_corresponding":false},{"id":1431920,"name":"Aakash M Rao","orcid":null,"position":36,"is_corresponding":false},{"id":1431921,"name":"Ashwin Salampuria","orcid":null,"position":37,"is_corresponding":false},{"id":1431420,"name":"Sina Akbarian","orcid":"0000-0002-0024-3999","position":38,"is_corresponding":false},{"id":1431922,"name":"Sepehr Asgarian","orcid":null,"position":39,"is_corresponding":false},{"id":1077751,"name":"Akanksha Arora","orcid":"0000-0001-6774-7887","position":40,"is_corresponding":false},{"id":1431421,"name":"Shubham Choudhury","orcid":"0000-0002-4509-4683","position":41,"is_corresponding":false},{"id":483569,"name":"Gajendra P. S. Raghava","orcid":"0000-0002-8902-2876","position":42,"is_corresponding":false},{"id":732089,"name":"Sherry Dong","orcid":null,"position":43,"is_corresponding":false},{"id":4926,"name":"Yuanfang Guan","orcid":"0000-0001-8275-2852","position":44,"is_corresponding":false},{"id":765820,"name":"Nan Yu","orcid":"0000-0002-0177-2067","position":45,"is_corresponding":false},{"id":225062,"name":"Hanrui Zhang","orcid":"0000-0001-8655-938X","position":46,"is_corresponding":false},{"id":1431923,"name":"Aniket Gupta","orcid":null,"position":47,"is_corresponding":false},{"id":1431422,"name":"Tenglong Li","orcid":"0000-0001-7666-1647","position":48,"is_corresponding":false},{"id":1431423,"name":"Rohan Singh","orcid":"0009-0005-2955-0852","position":49,"is_corresponding":false},{"id":1431424,"name":"Jouhyun Jeon","orcid":"0000-0003-2236-2849","position":50,"is_corresponding":false},{"id":1431924,"name":"Qayam Jetha","orcid":null,"position":51,"is_corresponding":false},{"id":1431425,"name":"Zhixiang Lu","orcid":"0000-0002-9954-9321","position":52,"is_corresponding":false},{"id":770681,"name":"Sumeet Patiyal","orcid":"0000-0003-1358-292X","position":53,"is_corresponding":false},{"id":1431925,"name":"Chandra Suda","orcid":null,"position":54,"is_corresponding":false},{"id":378252,"name":"Devan Jaganath","orcid":"0000-0002-8555-5667","position":0,"is_corresponding":true}],"reference_count":25,"raw_metadata":null,"created_at":"2026-07-19T02:52:55.809501Z","pmid":"41064697","pmcid":"PMC12502651","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":50.0,"fair_i":40.0,"fair_r":41.6667,"fair_zscore":0.4506,"fair_rationale":{"fair_score":45.83,"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":"The challenge deidentified training data, data dictionary, and links to the code and write-ups for the model submissions are available at www.synapse.org/TBcough","grounded":true,"rationale":"The only identifier given is a web URL (www.synapse.org/TBcough), not a persistent identifier scheme. [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":"The challenge was set up on Synapse (www.synapse.org/tbcough)","grounded":false,"rationale":"Synapse is named as the repository hosting the data, and it is a known research data repository. [downgraded to 'partial' — no verifiable quote from the paper] [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":"The challenge deidentified training data, data dictionary, and links to the code and write-ups for the model submissions are available at www.synapse.org/TBcough.","grounded":false,"rationale":"The statement points to a repository (Synapse) with a link, which is Colavizza category 3. [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":"Challenge teams were given direct access only to the training set, which included the raw peak cough sound recordings in WAV format, as well as associated age, sex, height, weight, smoking status, self-reported duration of cough, prior history of tuberculosis, common tuberculosis symptoms (hemoptysis, fever, night sweats, weight loss), heart rate, and temperature.","grounded":true,"rationale":"The dataset's content is described in running prose, not in an itemised inventory (section, 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":0.5,"verdict":"partial","evidence":"available at www.synapse.org/TBcough","grounded":true,"rationale":"The dataset URL 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":50.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"To access the data, register for a free Synapse account and then review and agree to the Synapse and CODA TB DREAM Challenge data use policies.","grounded":true,"rationale":"The data is accessible only after registration and agreement to policies, which is a specified precondition. [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":"To access the data, register for a free Synapse account and then review and agree to the Synapse and CODA TB DREAM Challenge data use policies.","grounded":true,"rationale":"The paper describes the access action (registration and agreement to policies) but does not explicitly label the access level. [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":1.0,"verdict":"yes","evidence":"To access the data, register for a free Synapse account and then review and agree to the Synapse and CODA TB DREAM Challenge data use policies.","grounded":true,"rationale":"The gatekeeper is an institutional process (Synapse account and data use policies), not a natural person. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No statement about how long the data will remain available is made. [majority verdict 'no' (2/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":40.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"raw peak cough sound recordings in WAV format","grounded":true,"rationale":"WAV is an open, non-proprietary 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No community standard (e.g., MIAME, ontology) is named for the data.","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 external resource identifier (e.g., DOI, accession) is given for data the study depends on. [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":41.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No license or reuse terms are stated for the data; only the article has a CC BY-NC-ND license. [majority verdict 'no' (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":1.0,"verdict":"yes","evidence":"The coughs were collected on an Android-based smartphone using the Hyfe Research app","grounded":true,"rationale":"The data production method names the specific instrument (Hyfe Research app) and platform (Android smartphone). [majority verdict 'yes' (4/5 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":0.5,"verdict":"partial","evidence":"The challenge deidentified training data, data dictionary, and links to the code and write-ups for the model submissions are available at www.synapse.org/TBcough.","grounded":false,"rationale":"A data dictionary is named as a documentation object that travels with the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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 given for the data snapshot.","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":"links to the code and write-ups for the model submissions are available at www.synapse.org/TBcough.","grounded":false,"rationale":"The code is available via a repository URL (Synapse), which is a machine-resolvable locator. [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":"grant U01 AI152087","grounded":true,"rationale":"An award number (U01 AI152087) is given for the funding. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No license or reuse terms are stated for the data; only the article has a CC BY-NC-ND license. [majority verdict 'no' (3/5 passes agreed)]","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The challenge deidentified training data, data dictionary, and links to the code and write-ups for the model submissions are available at www.synapse.org/TBcough","why":"The only identifier given is a web URL (www.synapse.org/TBcough), not a persistent identifier scheme. [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":"The challenge was set up on Synapse (www.synapse.org/tbcough)","why":"Synapse is named as the repository hosting the data, and it is a known research data repository. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"To access the data, register for a free Synapse account and then review and agree to the Synapse and CODA TB DREAM Challenge data use policies.","why":"The data is accessible only after registration and agreement to policies, which is a specified precondition. [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 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":"available at www.synapse.org/TBcough","why":"The dataset URL 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":"links to the code and write-ups for the model submissions are available at www.synapse.org/TBcough.","why":"The code is available via a repository URL (Synapse), which is a machine-resolvable locator. [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":null,"why":"No version token or date is given for the data snapshot.","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":"The challenge deidentified training data, data dictionary, and links to the code and write-ups for the model submissions are available at www.synapse.org/TBcough.","why":"The statement points to a repository (Synapse) with a link, which is Colavizza category 3. [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":"Challenge teams were given direct access only to the training set, which included the raw peak cough sound recordings in WAV format, as well as associated age, sex, height, weight, smoking status, self-reported duration of cough, prior history of tuberculosis, common tuberculosis symptoms (hemoptysis, fever, night sweats, weight loss), heart rate, and temperature.","why":"The dataset's content is described in running prose, not in an itemised inventory (section, 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":"To access the data, register for a free Synapse account and then review and agree to the Synapse and CODA TB DREAM Challenge data use policies.","why":"The paper describes the access action (registration and agreement to policies) but does not explicitly label the access level. [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 clinical / human-subjects, describe the data with OMOP CDM, CDISC SDTM or HL7 FHIR.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No community standard (e.g., MIAME, ontology) is named for the data.","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The challenge deidentified training data, data dictionary, and links to the code and write-ups for the model submissions are available at www.synapse.org/TBcough.","why":"A data dictionary is named as a documentation object that travels with the data. [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_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 external resource identifier (e.g., DOI, accession) is given for data the study depends on. [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 statement about how long the data will remain available is made. [majority verdict 'no' (2/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For 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).","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T13:30:20.530819Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}