2021
The application of artificial intelligence and data integration in COVID-19 studies: a scoping review
Guo Y, Zhang Y, Lyu T, Prosperi M, Wang F, Xu H, Bian J. The application of artificial intelligence and data integration in COVID-19 studies: a scoping review. Journal Of The American Medical Informatics Association 2021, 28: 2050-2067. PMID: 34151987, PMCID: PMC8344463, DOI: 10.1093/jamia/ocab098.Peer-Reviewed Original ResearchConceptsAI applicationsArtificial intelligenceData integrationHeterogeneous dataSocial media data analysisMost AI applicationsHeterogeneous data sourcesMedia data analysisProteomics data analysisAI algorithmsAI frameworkElectronic health recordsHeterogenous dataBiased algorithmsHealth recordsCOVID-19 researchData analysisSingle-source approachResearch topicData sourcesResearch areaIntelligenceSurveillance systemDifferent sourcesAlgorithmCOVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model
Wang J, Abu-El-Rub N, Gray J, Pham H, Zhou Y, Manion F, Liu M, Song X, Xu H, Rouhizadeh M, Zhang Y. COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model. Journal Of The American Medical Informatics Association 2021, 28: 1275-1283. PMID: 33674830, PMCID: PMC7989301, DOI: 10.1093/jamia/ocab015.Peer-Reviewed Original ResearchConceptsNatural language processing toolsCommon data modelLanguage processing toolsElectronic health recordsClinical natural language processing toolsData modelDeep learning-based modelProcessing toolsOMOP Common Data ModelPattern-based rulesObservational Medical Outcomes Partnership Common Data ModelLearning-based modelsSpecific information needsUse casesNLP toolsClinical textFree textExtensive evaluationDownloadable packageInformation needsHybrid approachResearch communityHealth recordsData sourcesHigh performance
2017
A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records.
Lee H, Jiang M, Wu Y, Shaffer C, Cleator J, Friedman E, Lewis J, Roden D, Denny J, Xu H. A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records. AMIA Joint Summits On Translational Science Proceedings 2017, 2017: 185-192. PMID: 28815128, PMCID: PMC5543340.Peer-Reviewed Original ResearchElectronic health recordsAdverse drug reactionsMachine learning-based methodsLearning-based methodsHealth recordsRule-based methodReasonable recallAutomatic identificationValuable data sourceAutomatic methodTemporality informationCertain adverse drug reactionsData sourcesIdentification of patientsPharmacogenomic studiesManual chart reviewInformatics approachAdverse eventsChart reviewDrug reactionsHigh precisionFunction-based methodScoring methodDifferent typesBleeding
2014
Identifying plausible adverse drug reactions using knowledge extracted from the literature
Shang N, Xu H, Rindflesch T, Cohen T. Identifying plausible adverse drug reactions using knowledge extracted from the literature. Journal Of Biomedical Informatics 2014, 52: 293-310. PMID: 25046831, PMCID: PMC4261011, DOI: 10.1016/j.jbi.2014.07.011.Peer-Reviewed Original ResearchConceptsPredication-based Semantic IndexingReflective Random IndexingLBD methodsNatural language processing toolsBiomedical literatureDrug-adverse event associationsLanguage processing toolsSemantic indexingElectronic health recordsRandom IndexingHuman reviewVast repositoryDiscovery methodsVolume of knowledgeProcessing toolsEvaluation setHealth recordsData sourcesEvent associationsIndexingDrug-effect relationshipsRepositoryLarge volumesADR associationsReasoning pathways
2012
DTome: a web-based tool for drug-target interactome construction
Sun J, Wu Y, Xu H, Zhao Z. DTome: a web-based tool for drug-target interactome construction. BMC Bioinformatics 2012, 13: s7. PMID: 22901092, PMCID: PMC3372450, DOI: 10.1186/1471-2105-13-s9-s7.Peer-Reviewed Original ResearchConceptsWeb-based toolUser-friendly web interfaceWeb-based queriesRich data sourceDifferent knowledge basesDatabase schemaWeb interfaceVisualization processKnowledge basesComputational workflowDiscovery processData sourcesNetworkDrug-target interactionsDrugs' primary targetsDrug-target networkWorkflowEarly-stage drug discoveryNetwork analysisQueriesToolPromising approachDrug discovery processSchemaDetailed network analysis