2020
Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events
Li F, Du J, He Y, Song H, Madkour M, Rao G, Xiang Y, Luo Y, Chen H, Liu S, Wang L, Liu H, Xu H, Tao C. Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. Journal Of The American Medical Informatics Association 2020, 27: 1046-1056. PMID: 32626903, PMCID: PMC7647306, DOI: 10.1093/jamia/ocaa058.Peer-Reviewed Original ResearchMeSH KeywordsBiological OntologiesDecision Support Systems, ClinicalElectronic Health RecordsHumansNatural Language ProcessingSemantic WebTimeConceptsTime Event OntologyComplex temporal relationsEvent ontologyNatural language processing fieldTemporal relationsTime-related queriesInformation annotationProcessing fieldTemporal informationData propertiesRelation representationClinical narrativesSemantic representationElectronic health record dataRich setHealth record dataOntologyStrong capabilityReasoningSetQueriesOrder relationRecord dataRepresentationPrimitives
2017
Lightweight predicate extraction for patient-level cancer information and ontology development
Amith M, Song H, Zhang Y, Xu H, Tao C. Lightweight predicate extraction for patient-level cancer information and ontology development. BMC Medical Informatics And Decision Making 2017, 17: 73. PMID: 28699547, PMCID: PMC5506564, DOI: 10.1186/s12911-017-0465-x.Peer-Reviewed Original ResearchMeSH KeywordsBiological OntologiesHumansMedlinePlusNatural Language ProcessingNeoplasmsPublic HealthConceptsOntological knowledgebaseKnowledge triplesInformation extraction toolsDevelopment of ontologiesNatural language domainRDF representationSoftware libraryOntology developmentCustom applicationsOntologyDevelopment processExtraction toolAccurate extractionPublic health domainKnowledgebaseTextual sourcesTriplesKnowledgebasesHealth domainsToolExtractionTaskMethodsThis paperMedlinePlusDomainFinding useful data across multiple biomedical data repositories using DataMed
Ohno-Machado L, Sansone S, Alter G, Fore I, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj A, Bell E, Soysal E, Zong N, Kim H. Finding useful data across multiple biomedical data repositories using DataMed. Nature Genetics 2017, 49: 816-819. PMID: 28546571, PMCID: PMC6460922, DOI: 10.1038/ng.3864.Peer-Reviewed Original ResearchMeSH KeywordsBiological OntologiesBiomedical ResearchComputational BiologyDatabases, FactualHumansMetadataSoftwareSystems IntegrationConceptsBiomedical data repositoriesHealth big dataData setsKnowledge discoveryBig dataMultiple repositoriesSearch enginesData indexFAIR principlesDataMedData repositoryService providersKnowledge initiativesKnowledge expertsBiomedical research communityResearch communityRepositoryScience landscapeUseful dataInteroperabilityMetadataFindabilitySetEngineDataExpressing Biomedical Ontologies in Natural Language for Expert Evaluation.
Amith M, Manion F, Harris M, Zhang Y, Xu H, Tao C. Expressing Biomedical Ontologies in Natural Language for Expert Evaluation. 2017, 245: 838-842. PMID: 29295217, PMCID: PMC6644701.Peer-Reviewed Original Research
2016
Extracting drug-enzyme relation from literature as evidence for drug drug interaction
Zhang Y, Wu H, Du J, Xu J, Wang J, Tao C, Li L, Xu H. Extracting drug-enzyme relation from literature as evidence for drug drug interaction. Journal Of Biomedical Semantics 2016, 7: 11. PMID: 26955465, PMCID: PMC4780188, DOI: 10.1186/s13326-016-0052-6.Peer-Reviewed Original Research
2015
Named Entity Recognition in Chinese Clinical Text Using Deep Neural Network.
Wu Y, Jiang M, Lei J, Xu H. Named Entity Recognition in Chinese Clinical Text Using Deep Neural Network. 2015, 216: 624-8. PMID: 26262126, PMCID: PMC4624324.Peer-Reviewed Original ResearchConceptsDeep neural networksLarge unlabeled corpusNamed Entity RecognitionWord embeddingsUnlabeled corpusUnsupervised learningEntity recognitionNeural networkNatural language processing technologyNovel deep learning methodLanguage processing technologyDeep learning methodsUnsupervised feature learningFeature engineering approachImportant healthcare informationChinese clinical textTypes of entitiesFeature learningNER taskClinical textLearning methodsClinical documentsCRF modelHealthcare informationFree text