2023
An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C)
Liu S, Wen A, Wang L, He H, Fu S, Miller R, Williams A, Harris D, Kavuluru R, Liu M, Abu-el-Rub N, Schutte D, Zhang R, Rouhizadeh M, Osborne J, He Y, Topaloglu U, Hong S, Saltz J, Schaffter T, Pfaff E, Chute C, Duong T, Haendel M, Fuentes R, Szolovits P, Xu H, Liu H. An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). Journal Of The American Medical Informatics Association 2023, 30: 2036-2040. PMID: 37555837, PMCID: PMC10654844, DOI: 10.1093/jamia/ocad134.Peer-Reviewed Original ResearchConceptsNatural language processingNLP modelsClinical natural language processingNatural language processing frameworkEHR-based clinical researchMulti-site settingSymptom extractionProcessing frameworkNLP frameworkLanguage processingNLP solutionMulti-site dataAlgorithm robustnessMethodology advancementsResearch communityTranslational research communityNational COVID Cohort CollaborativeCase demonstrationProcess heterogeneityFrameworkAnnotationCOVID cohort
2022
MedTator: a serverless annotation tool for corpus development
He H, Fu S, Wang L, Liu S, Wen A, Liu H. MedTator: a serverless annotation tool for corpus development. Bioinformatics 2022, 38: 1776-1778. PMID: 34983060, PMCID: PMC10060696, DOI: 10.1093/bioinformatics/btab880.Peer-Reviewed Original ResearchConceptsAnnotation toolInteractive user interfaceApache 2.0 licenseDocument annotationUser interfaceAnnotation taskSource codeAdvanced featuresDifficulty of useAnnotation corpusCorpus developmentCorpus annotationCore stepsSupplementary dataVariety of needsAnnotationClinical research applicationsSummarizationResearch applicationsToolConsiderable timeTaskBioinformaticsTutorialCode