{"doi":"10.1017/cts.2025.10116","title":"Development and validation of natural language processing algorithms in the national ENACT network","abstract":"Objective: Electronic Health Record (EHR) data are critical for advancing translational research and AI technologies. The ENACT network offers access to structured EHR data across 57 CTSA hubs. However, substantial information is contained in clinical narratives, requiring natural language processing (NLP) for research. The ENACT NLP Working Group was formed to make NLP-derived clinical information accessible and queryable across the network. Methods: We established the ENACT NLP Working Group with 13 sites selected based on criteria including clinical notes access, IT infrastructure, NLP expertise, and institutional support. We divided sites into five focus groups targeting clinical tasks within disease contexts. Each focus group consisted of two development sites and two validation sites. We extended the ENACT ontology to standardize NLP-derived data and conducted multisite evaluations using the Open Health Natural Language Processing (OHNLP) Toolkit. Results: The working group achieved 100% site retention and deployed NLP infrastructure across all sites. We developed and validated NLP algorithms for rare disease phenotyping, social determinants of health, opioid use disorder, sleep phenotyping, and delirium phenotyping. Performance varied across sites (F1 scores 0.53-0.96), highlighting data heterogeneity impacts. We extended the ENACT common data model and ontology to incorporate NLP-derived data while maintaining Shared Health Research Informatics NEtwork (SHRINE) compatibility. Conclusion: This demonstrates feasibility of deploying NLP infrastructure across large, federated networks. The focus group approach proved more practical than general-purpose approaches. Key lessons include the challenge of data heterogeneity and importance of collaborative governance. This work also provides a foundation that other networks can build on to implement NLP capabilities for translational research.","journal":"Journal of Clinical and Translational Science","year":2025,"id":573103,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":0.0,"corpus_rank":10163,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5901,"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":4.1667,"fair_percentile":4.891470498318557,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1019133,"name":"Jordan Hilsman","orcid":null,"position":1,"is_corresponding":false},{"id":1210969,"name":"Chenyu Li","orcid":"0000-0001-7434-6571","position":2,"is_corresponding":false},{"id":225292,"name":"Michele Morris","orcid":"0000-0002-3255-5727","position":3,"is_corresponding":false},{"id":1004276,"name":"Paul M. Heider","orcid":"0000-0002-1589-4567","position":4,"is_corresponding":false},{"id":251072,"name":"Sunyang Fu","orcid":"0000-0003-1691-5179","position":5,"is_corresponding":false},{"id":725623,"name":"Min Ji Kwak","orcid":"0000-0003-2778-3984","position":6,"is_corresponding":false},{"id":251079,"name":"Andrew Wen","orcid":"0000-0001-9090-8028","position":7,"is_corresponding":false},{"id":1440101,"name":"Joseph R. Applegate","orcid":null,"position":8,"is_corresponding":false},{"id":1439699,"name":"Liwei Wang","orcid":"0009-0000-1573-1015","position":9,"is_corresponding":false},{"id":274494,"name":"Elmer V. Bernstam","orcid":"0000-0001-7643-791X","position":10,"is_corresponding":false},{"id":49903,"name":"Hongfang Liu","orcid":"0000-0003-2570-3741","position":11,"is_corresponding":false},{"id":536554,"name":"Jack Chang","orcid":"0000-0002-5645-0014","position":12,"is_corresponding":false},{"id":471653,"name":"Daniel R. Harris","orcid":"0000-0001-9139-3433","position":13,"is_corresponding":false},{"id":1295120,"name":"Alexandria Corbeau","orcid":null,"position":14,"is_corresponding":false},{"id":621077,"name":"Darren W. Henderson","orcid":"0000-0001-6198-1912","position":15,"is_corresponding":false},{"id":37896,"name":"John D. Osborne","orcid":"0000-0002-0851-1150","position":16,"is_corresponding":false},{"id":436136,"name":"Richard Kennedy","orcid":"0000-0003-4638-126X","position":17,"is_corresponding":false},{"id":1415621,"name":"Nelly-Estefanie Garduno-Rapp","orcid":null,"position":18,"is_corresponding":false},{"id":59496,"name":"Justin F. Rousseau","orcid":"0000-0002-2817-9124","position":19,"is_corresponding":false},{"id":320508,"name":"Chao Yan","orcid":"0000-0002-6719-1388","position":20,"is_corresponding":false},{"id":692041,"name":"You Chen","orcid":"0000-0001-8232-8840","position":21,"is_corresponding":false},{"id":519213,"name":"Mayur B. Patel","orcid":"0000-0001-5230-0871","position":22,"is_corresponding":false},{"id":1453397,"name":"Tyler J. Murphy","orcid":null,"position":23,"is_corresponding":false},{"id":320509,"name":"Bradley Malin","orcid":"0000-0003-3040-5175","position":24,"is_corresponding":false},{"id":1452889,"name":"Chan Mi Park","orcid":"0000-0001-6404-4174","position":25,"is_corresponding":false},{"id":371399,"name":"Jungwei Fan","orcid":"0000-0001-6349-3752","position":26,"is_corresponding":false},{"id":251080,"name":"Sunghwan Sohn","orcid":"0000-0001-8256-2602","position":27,"is_corresponding":false},{"id":869868,"name":"Sandeep R. Pagali","orcid":"0000-0002-0838-1026","position":28,"is_corresponding":false},{"id":1211974,"name":"Yifan Peng","orcid":"0000-0003-0667-2599","position":29,"is_corresponding":false},{"id":1164015,"name":"Aman Pathak","orcid":null,"position":30,"is_corresponding":false},{"id":285007,"name":"Yonghui Wu","orcid":"0000-0002-6780-6135","position":31,"is_corresponding":false},{"id":554569,"name":"Zongqi Xia","orcid":"0000-0003-1500-2589","position":32,"is_corresponding":false},{"id":913238,"name":"Salvatore Loguercio","orcid":"0000-0002-7544-2992","position":33,"is_corresponding":false},{"id":413400,"name":"Steven E. Reís","orcid":"0000-0001-8023-0102","position":34,"is_corresponding":false},{"id":225296,"name":"Shyam Visweswaran","orcid":"0000-0002-2079-8684","position":35,"is_corresponding":false},{"id":393408,"name":"Yanshan Wang","orcid":"0000-0003-4433-7839","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:57:32.445190Z","pmid":"40979101","pmcid":"PMC12444719","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":0.0,"fair_a":0.0,"fair_i":20.0,"fair_r":16.6667,"fair_zscore":-1.1986,"fair_rationale":{"fair_score":4.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":0.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The 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[majority verdict 'no' (2/5 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":"The OHNLP Toolkit is available at the OHNLP website (https://ohnlp.org/).","grounded":true,"rationale":"The paper provides a URL for the OHNLP Toolkit, a software resource other than the study's own dataset. [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":16.67,"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 is named for the data; the article's CC-BY license applies to the paper, not the data.","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":"the site deploys the OHNLP Toolkit","grounded":false,"rationale":"The paper names the OHNLP Toolkit as the specific software used to process the data. 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[majority verdict 'no' (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 research reported in this publication was supported by the National Institutes of Health under award numbers U01TR002062, UL1TR001998, UM1TR004906, U01TR002628, UL1TR003163, UL1TR001857, U24TR004111, 30TR002103, UL1TR002001, UL1TR002377, and UM1TR004407 from the National Center for Advancing Translational Sciences, award numbers RF1AG072799, R01AG060993, R01AG077017, and R01AG068007 from the National Institute on Aging, award number R01LM014306 from the National Library of Medicine, award number R01GM141476 from the National Institute of General Medical Sciences, and the Reynolds and Reynolds Foundation.","grounded":true,"rationale":"The paper lists multiple specific award numbers from named funders.","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":"no","current":0.0,"evidence":null,"why":"The paper assigns no persistent identifier to its own dataset; the article DOI is for the paper.","gain":16.67,"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":"no","current":0.0,"evidence":null,"why":"No repository is named as holding the study's own data; the paper states the data cannot be shared.","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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The patient-level electronic health record data cannot be shared due to privacy and legal concerns.","why":"The paper explicitly states the data cannot be shared, so no followable route exists.","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":"No license is named for the data; the article's CC-BY license applies to the paper, not the data.","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the 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":"no","current":0.0,"evidence":null,"why":"No identifier for the study's own dataset appears in the reference list or body text.","gain":8.33,"priority":"important","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. 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[majority verdict 'no' (4/5 passes agreed)]","gain":8.33,"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":"Neither a version token nor a date is given to identify a snapshot of the data.","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":"no","current":0.0,"evidence":"The patient-level electronic health record data cannot be shared due to privacy and legal concerns.","why":"The data-availability statement declares the data cannot be shared, offering no route, which corresponds to Colavizza category 0.","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not provide an itemised inventory of files, records, or variables for the dataset.","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'. 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[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_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No documentation object such as a README or codebook is named as accompanying the data.","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":"The patient-level electronic health record data cannot be shared due to privacy and legal concerns.","why":"The paper states the data cannot be shared and names no gatekeeper of any kind.","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 address when the data are 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":"2026-07-20T13:57:43.672134Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}