2018
DataMed – an open source discovery index for finding biomedical datasets
Chen X, Gururaj A, Ozyurt B, Liu R, Soysal E, Cohen T, Tiryaki F, Li Y, Zong N, Jiang M, Rogith D, Salimi M, Kim H, Rocca-Serra P, Gonzalez-Beltran A, Farcas C, Johnson T, Margolis R, Alter G, Sansone S, Fore I, Ohno-Machado L, Grethe J, Xu H. DataMed – an open source discovery index for finding biomedical datasets. Journal Of The American Medical Informatics Association 2018, 25: 300-308. PMID: 29346583, PMCID: PMC7378878, DOI: 10.1093/jamia/ocx121.Peer-Reviewed Original ResearchIngestion pipelineBiomedical datasetsSearch enginesBiomedical domainAdvanced natural language processingRelevant datasetsUser-entered queryData discovery systemUnified metadata modelData ingestion pipelinesNatural language processingOpen-source packageRetrieval engineTerminology servicesMetadata modelMetadata informationDiscovery systemData reuseDataMedBenchmark datasetsBiomedical dataData indexAverage precisionLanguage processingSource package
2017
Ensembles of NLP Tools for Data Element Extraction from Clinical Notes.
Kuo T, Rao P, Maehara C, Doan S, Chaparro J, Day M, Farcas C, Ohno-Machado L, Hsu C. Ensembles of NLP Tools for Data Element Extraction from Clinical Notes. AMIA Annual Symposium Proceedings 2017, 2016: 1880-1889. PMID: 28269947, PMCID: PMC5333200.Peer-Reviewed Original ResearchConceptsNatural language processingNLP toolsElectronic health recordsData elementsConcept extractionLanguage processingEnsemble methodDiverse conceptsEvaluation resultsHealth recordsElement extractionClinical notesPlausible solutionToolPipelineExtractionPerformanceEnsembleExtraction performanceConceptNarrative textProcessingText
2014
Natural Language Processing in Biomedicine: A Unified System Architecture Overview
Doan S, Conway M, Phuong T, Ohno-Machado L. Natural Language Processing in Biomedicine: A Unified System Architecture Overview. Methods In Molecular Biology 2014, 1168: 275-294. PMID: 24870142, DOI: 10.1007/978-1-4939-0847-9_16.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsNatural language processingNLP systemsLanguage processingClinical natural language processingBiomedical natural language processingClinical decision supportImportant data sourceArchitectural viewsStructured data fieldsArchitecture overviewData sharingNLP toolsGeneral architectureDecision supportKnowledge resourcesBackground knowledgeData fieldsCollaborative workSystem evaluationData sourcesCurrent research effortsElectronic medical recordsResearch effortsProcessingQuality assurance
2011
Natural language processing: an introduction
Nadkarni PM, Ohno-Machado L, Chapman WW. Natural language processing: an introduction. Journal Of The American Medical Informatics Association 2011, 18: 544-551. PMID: 21846786, PMCID: PMC3168328, DOI: 10.1136/amiajnl-2011-000464.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements