{"doi":"10.1093/jamia/ocad049","title":"Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions","abstract":"OBJECTIVE: We aimed to develop a distributed, immutable, and highly available cross-cloud blockchain system to facilitate federated data analysis activities among multiple institutions. MATERIALS AND METHODS: We preprocessed 9166 COVID-19 Structured Query Language (SQL) code, summary statistics, and user activity logs, from the GitHub repository of the Reliable Response Data Discovery for COVID-19 (R2D2) Consortium. The repository collected local summary statistics from participating institutions and aggregated the global result to a COVID-19-related clinical query, previously posted by clinicians on a website. We developed both on-chain and off-chain components to store/query these activity logs and their associated queries/results on a blockchain for immutability, transparency, and high availability of research communication. We measured run-time efficiency of contract deployment, network transactions, and confirmed the accuracy of recorded logs compared to a centralized baseline solution. RESULTS: The smart contract deployment took 4.5 s on an average. The time to record an activity log on blockchain was slightly over 2 s, versus 5-9 s for baseline. For querying, each query took on an average less than 0.4 s on blockchain, versus around 2.1 s for baseline. DISCUSSION: The low deployment, recording, and querying times confirm the feasibility of our cross-cloud, blockchain-based federated data analysis system. We have yet to evaluate the system on a larger network with multiple nodes per cloud, to consider how to accommodate a surge in activities, and to investigate methods to lower querying time as the blockchain grows. CONCLUSION: Blockchain technology can be used to support federated data analysis among multiple institutions.","journal":"Journal of the American Medical Informatics Association","year":2023,"id":338152,"datarank":0.6228282495017599,"base_score":2.8903717578961645,"endowment":2.8903717578961645,"self_citation_contribution":0.4335557636844247,"citation_network_contribution":0.18927248581733516,"self_endowment_contribution":0.4335557636844247,"citer_contribution":0.18927248581733516,"corpus_percentile":68.2834377659163,"corpus_rank":4101,"citation_count":17,"citer_count":9,"citers_with_citation_signal":6,"citers_with_endowment":6,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7172,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":12.5,"fair_percentile":28.767960868236013,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1070538,"name":"Anh T. Pham","orcid":"0000-0002-5143-1498","position":1,"is_corresponding":false},{"id":936341,"name":"Maxim Edelson","orcid":null,"position":2,"is_corresponding":false},{"id":13662,"name":"Jihoon Kim","orcid":"0000-0002-5351-238X","position":3,"is_corresponding":false},{"id":1070539,"name":"Jason R. Chan","orcid":"0000-0003-1618-5516","position":4,"is_corresponding":false},{"id":1071100,"name":"Yash P. Gupta","orcid":null,"position":5,"is_corresponding":false},{"id":14419,"name":"Lucila Ohno‐Machado","orcid":"0000-0002-8005-7327","position":6,"is_corresponding":false},{"id":728980,"name":"David M. Anderson","orcid":"0000-0003-4755-9955","position":7,"is_corresponding":false},{"id":729488,"name":"Chandrasekar Balacha","orcid":null,"position":8,"is_corresponding":false},{"id":464276,"name":"Tyler Bath","orcid":"0000-0003-2601-178X","position":9,"is_corresponding":false},{"id":349921,"name":"Sally L. Baxter","orcid":"0000-0002-5271-7690","position":10,"is_corresponding":false},{"id":728981,"name":"Andrea Becker-Pennrich","orcid":"0000-0003-2915-9501","position":11,"is_corresponding":false},{"id":360565,"name":"Douglas S. Bell","orcid":"0000-0002-5063-8294","position":12,"is_corresponding":false},{"id":274494,"name":"Elmer V. Bernstam","orcid":"0000-0001-7643-791X","position":13,"is_corresponding":false},{"id":1071101,"name":"Chau Ngan","orcid":null,"position":14,"is_corresponding":false},{"id":729487,"name":"Michele E. Day","orcid":null,"position":15,"is_corresponding":false},{"id":446990,"name":"Jason N. Doctor","orcid":"0000-0003-3661-8745","position":16,"is_corresponding":false},{"id":11351,"name":"Scott L. DuVall","orcid":"0000-0002-4898-3865","position":17,"is_corresponding":false},{"id":385248,"name":"Robert El‐Kareh","orcid":"0000-0003-3158-5681","position":18,"is_corresponding":false},{"id":729492,"name":"Renato Florian","orcid":null,"position":19,"is_corresponding":false},{"id":512951,"name":"Robert W Follett","orcid":"0000-0003-1618-2817","position":20,"is_corresponding":false},{"id":728983,"name":"Benjamin P. Geisler","orcid":"0000-0003-1704-6067","position":21,"is_corresponding":false},{"id":728984,"name":"Alessandro Ghigi","orcid":"0000-0002-5105-3415","position":22,"is_corresponding":false},{"id":90565,"name":"Assaf Gottlieb","orcid":"0000-0003-4904-631X","position":23,"is_corresponding":false},{"id":568242,"name":"Ludwig Christian Hinske","orcid":"0000-0001-7273-5899","position":24,"is_corresponding":false},{"id":713971,"name":"Zhaoxian Hu","orcid":"0000-0002-5339-4942","position":25,"is_corresponding":false},{"id":256913,"name":"Diana Ir","orcid":null,"position":26,"is_corresponding":false},{"id":66208,"name":"Xiaoqian Jiang","orcid":"0000-0001-9933-2205","position":27,"is_corresponding":false},{"id":3950,"name":"Katherine K Kim","orcid":"0000-0001-5766-3938","position":28,"is_corresponding":false},{"id":728985,"name":"Tara K. Knight","orcid":"0000-0003-2755-0494","position":30,"is_corresponding":false},{"id":728986,"name":"Jejo Koola","orcid":"0000-0001-5171-8475","position":31,"is_corresponding":false},{"id":36633,"name":"Nelson Lee","orcid":"0000-0002-0783-6607","position":33,"is_corresponding":false},{"id":20385,"name":"Ulrich Mansmann","orcid":"0000-0002-9955-8906","position":34,"is_corresponding":false},{"id":11398,"name":"Michael E. Matheny","orcid":"0000-0003-3217-4147","position":35,"is_corresponding":false},{"id":341928,"name":"Daniella Meeker","orcid":"0000-0002-1034-7628","position":36,"is_corresponding":false},{"id":728987,"name":"Zongyang Mou","orcid":"0000-0003-3271-4596","position":37,"is_corresponding":false},{"id":568240,"name":"Larissa Neumann","orcid":"0000-0001-6845-5413","position":38,"is_corresponding":false},{"id":27728,"name":"Nghia Nguyen","orcid":"0000-0002-4043-0430","position":39,"is_corresponding":false},{"id":1071102,"name":"Anderson Nick","orcid":null,"position":40,"is_corresponding":false},{"id":465238,"name":"Eunice Park","orcid":"0000-0003-1159-2374","position":42,"is_corresponding":false},{"id":311023,"name":"Paulina Paul","orcid":"0000-0002-2528-5917","position":43,"is_corresponding":false},{"id":232378,"name":"Mark J. Pletcher","orcid":"0000-0002-6966-1312","position":44,"is_corresponding":false},{"id":707328,"name":"Kai Post","orcid":"0000-0003-1002-3989","position":45,"is_corresponding":false},{"id":728990,"name":"Clemens Rieder","orcid":"0000-0001-9355-7534","position":46,"is_corresponding":false},{"id":728991,"name":"Clemens Scherer","orcid":"0000-0003-2816-6793","position":47,"is_corresponding":false},{"id":277997,"name":"Lisa M. Schilling","orcid":"0000-0002-6878-189X","position":48,"is_corresponding":false},{"id":1070540,"name":"Andrey Coatrini Soares","orcid":"0000-0003-4601-3555","position":49,"is_corresponding":false},{"id":360564,"name":"Spencer L. SooHoo","orcid":"0000-0003-3709-5659","position":50,"is_corresponding":false},{"id":728993,"name":"Ekin Soysal","orcid":"0009-0001-4534-0055","position":51,"is_corresponding":false},{"id":1071103,"name":"Covington Steven","orcid":null,"position":52,"is_corresponding":false},{"id":362501,"name":"Brian Tep","orcid":null,"position":53,"is_corresponding":false},{"id":382735,"name":"Brian C. 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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 deidentified version of data used in this article will be shared on reasonable request to the corresponding author.","why":"The statement points to a person (Colavizza category 1), not a repository record.","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":"We preprocessed 9166 COVID-19 Structured Query Language (SQL) code, summary statistics, and user activity logs, from the GitHub repository of the Reliable Response Data Discovery for COVID-19 (R2D2) Consortium.","why":"Dataset content is described in running prose, not in an itemized inventory (section, table, or list). [majority verdict 'partial' (4/5 passes agreed)]","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 deidentified version of data used in this article will be shared on reasonable request to the corresponding author.","why":"No access-level label is applied, but the text describes the action of requesting data from the author. [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 FAIRsharing-registered data/metadata standard (e.g., MIAME, BIDS, an ontology) is named for the data.","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":"we adopted the Go-Ethereum (Geth) implementation, and used a Proof-of-Authority (PoA) consensus protocol Clique","why":"Specific tools and versions (Geth, Clique, Solidity, etc.) are named for data production. [downgraded to 'partial' — no verifiable quote from the paper] [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":"partial","current":0.5,"evidence":"Table 1. Information captured from the COVID-19 consortium private GitHub repository","why":"Variable definitions are provided in Table 1 inside the article, but no documentation object (README, codebook) is said to travel with the data. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human clinical / human-subjects data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The deidentified version of data used in this article will be shared on reasonable request to the corresponding author.","why":"The gatekeeper is the natural person (corresponding author) with no institutional committee named.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifier (accession, DOI, RRID, etc.) is given for any external resource the data depends on.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No sentence states when the data become available or how long they persist.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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).","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.","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":"2026-07-20T12:00:45.046456Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}