{"doi":"10.1093/jamiaopen/ooaf086","title":"Data harmonization framework for neonatal hypoxic-ischemic encephalopathy studies","abstract":"Abstract Objectives To develop a data harmonization framework for neonatal hypoxic-ischemic encephalopathy (HIE) studies and demonstrate its suitability for prognostic biomarker development. Materials and Methods Variables were first categorized by chronological stages and then by medical topics. We created a dictionary to harmonize variable names and value coding. We began by merging comprehensive data from 2 landmark nationwide therapeutic hypothermia for HIE trials (2008-2016, 21 sites) in the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Neonatal Research Network (NRN). The 2 datasets differ in available variables, variable naming and coding, necessitating harmonization. To demonstrate the utility of this data harmonization framework, we computed the distributions of variables and ranked them by the strength of associations with 18- to 22-month outcomes. Associations were measured using Pearson’s correlation analysis. Outcomes were defined as (a) a 5-class variable: survivors with normal, mild, moderate, severe disability, or death and (b) the Bayley-III Scales. Results We created a dictionary of 1181 variables on 532 patients across 5 chronologic categories and 60 medical subcategories. The distribution of major predictive and outcome variables, and the variables strongly associated with neurodevelopmental outcomes at 18-22 months were presented. The modified Sarnat scores at the Post-intervention and NICU-discharge stage, and the NRN pattern of MRI injury score showed strong associations with outcome variables. Conclusion We designed a data harmonization framework specifically for HIE. Our initial effort in merging 2 iconic clinical trials shows strong predictor-outcome associations, allowing subsequent development of advanced prognostic biomarkers of neonatal HIE.","journal":"JAMIA Open","year":2025,"id":546697,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":22.178386323199504,"corpus_rank":9377,"citation_count":1,"citer_count":1,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8315,"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":70.8333,"fair_percentile":91.99021705900336,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":871048,"name":"Anna N. Foster","orcid":"0000-0002-1838-7237","position":1,"is_corresponding":false},{"id":439241,"name":"Scott A. McDonald","orcid":"0000-0002-0054-1099","position":2,"is_corresponding":false},{"id":957561,"name":"Rutvi Vyas","orcid":"0000-0001-7177-0721","position":3,"is_corresponding":false},{"id":1438791,"name":"Azra A. Ashraf","orcid":"0009-0000-1277-4423","position":4,"is_corresponding":false},{"id":1014952,"name":"Rina Bao","orcid":"0000-0003-2367-2590","position":5,"is_corresponding":false},{"id":1438792,"name":"Lena Tran","orcid":"0000-0002-3676-0488","position":6,"is_corresponding":false},{"id":1439198,"name":"Ankush Kesri","orcid":null,"position":7,"is_corresponding":false},{"id":1438793,"name":"Erfan Darzidehkalani","orcid":"0000-0002-6003-0119","position":8,"is_corresponding":false},{"id":1227333,"name":"Matheus Dorigatti Soldatelli","orcid":"0000-0002-1544-4398","position":9,"is_corresponding":false},{"id":690696,"name":"Jeanette O’Donnell Auman","orcid":"0000-0002-4829-199X","position":10,"is_corresponding":false},{"id":430124,"name":"Janet S. Soul","orcid":"0000-0001-6998-7753","position":11,"is_corresponding":false},{"id":330801,"name":"Lina F. Chalak","orcid":"0000-0001-5496-3257","position":12,"is_corresponding":false},{"id":230765,"name":"C. Michael Cotten","orcid":"0000-0002-8569-9003","position":13,"is_corresponding":false},{"id":439242,"name":"Seetha Shankaran","orcid":"0000-0001-5512-9571","position":14,"is_corresponding":false},{"id":230773,"name":"Abbot R. Laptook","orcid":"0000-0001-9848-3466","position":15,"is_corresponding":false},{"id":244777,"name":"P. Ellen Grant","orcid":"0000-0003-1005-4013","position":16,"is_corresponding":false},{"id":244776,"name":"Yangming Ou","orcid":"0000-0002-7726-6208","position":17,"is_corresponding":false},{"id":230772,"name":"Michele C. Walsh","orcid":"0000-0003-0203-4274","position":22,"is_corresponding":false},{"id":355529,"name":"Eric C. Eichenwald","orcid":"0000-0003-3052-9127","position":23,"is_corresponding":false},{"id":239391,"name":"William E. Truog","orcid":null,"position":24,"is_corresponding":false},{"id":356102,"name":"Stephanie L. Merhar","orcid":"0000-0002-3331-4220","position":25,"is_corresponding":false},{"id":1439199,"name":"Brenda L B Poindexter","orcid":null,"position":26,"is_corresponding":false},{"id":1438794,"name":"Lili He","orcid":"0000-0003-0198-362X","position":27,"is_corresponding":false},{"id":235656,"name":"Shannon E. G. Hamrick","orcid":"0000-0002-6294-3480","position":29,"is_corresponding":false},{"id":234060,"name":"Gregory M. Sokol","orcid":null,"position":30,"is_corresponding":false},{"id":498809,"name":"Sara V. Bates","orcid":"0000-0002-2390-813X","position":31,"is_corresponding":false},{"id":230762,"name":"Pablo J. Sánchez","orcid":"0000-0003-2437-1247","position":32,"is_corresponding":false},{"id":439238,"name":"Edward G. Shepherd","orcid":"0000-0001-6816-7059","position":33,"is_corresponding":false},{"id":282816,"name":"Mai‐Lan Ho","orcid":"0000-0002-9455-1350","position":34,"is_corresponding":false},{"id":230767,"name":"Krisa P. Van Meurs","orcid":"0000-0002-9242-1480","position":36,"is_corresponding":false},{"id":238382,"name":"Susan R. Hintz","orcid":"0000-0001-7023-4433","position":37,"is_corresponding":false},{"id":506450,"name":"Sonia L. Bonifacio","orcid":"0000-0002-4171-7900","position":38,"is_corresponding":false},{"id":695360,"name":"Ivan D. Frantz","orcid":"0000-0002-2200-4286","position":39,"is_corresponding":false},{"id":409094,"name":"Namasivayam Ambalavanan","orcid":"0000-0003-0731-9092","position":40,"is_corresponding":false},{"id":230763,"name":"Edward F. Bell","orcid":"0000-0002-5568-0889","position":41,"is_corresponding":false},{"id":1025275,"name":"Patrick J. McNamara","orcid":"0000-0001-7648-8872","position":42,"is_corresponding":false},{"id":230771,"name":"Kristi L. Watterberg","orcid":"0000-0001-6432-1928","position":43,"is_corresponding":false},{"id":234054,"name":"Carl T. D’Angio","orcid":null,"position":44,"is_corresponding":false},{"id":265465,"name":"Jon E. 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We created a dictionary to harmonize variable names and value coding.","why":"The production of the harmonized data is described in generic terms without naming specific instruments or software versions. [majority verdict 'partial' (2/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The definition of the metadata and the data dictionary of the framework is maintained as spreadsheets and REDCap format and can be found in Supplementary Material S1, S2, and S4 .","why":"The variable definitions are provided inside the article's supplementary material, not as a separate documentation object shipped with the data; this is partial (inside the article). [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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper's own data (harmonized dictionary and results) are not sensitive and are publicly available; no gatekeeper of any kind is named for this study's data.","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 mention how long the data will be retained or any persistence commitment; it only states the data are available now. [majority verdict 'no' (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 neuroimaging data, deposit in OpenNeuro or NeuroVault.","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 neuroimaging data, deposit in OpenNeuro or NeuroVault.","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. Prefer open neuroimaging formats such as NIfTI or BIDS.","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 neuroimaging repository accession (e.g. from OpenNeuro or NeuroVault) in the reference list.","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."],"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":"2026-07-20T13:45:58.891636Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}