2024
NLP Applications—Other Biomedical Texts
Roberts K, Xu H, Demner Fushman D. NLP Applications—Other Biomedical Texts. Cognitive Informatics In Biomedicine And Healthcare 2024, 429-444. DOI: 10.1007/978-3-031-55865-8_15.Peer-Reviewed Original ResearchMapping Clinical Documents to the Logical Observation Identifiers, Names and Codes (LOINC) Document Ontology using Electronic Health Record Systems Structured Metadata.
Khan H, Mosa A, Paka V, Rana M, Mandhadi V, Islam S, Xu H, McClay J, Sarker S, Rao P, Waitman L. Mapping Clinical Documents to the Logical Observation Identifiers, Names and Codes (LOINC) Document Ontology using Electronic Health Record Systems Structured Metadata. AMIA Annual Symposium Proceedings 2024, 2023: 1017-1026. PMID: 38222329, PMCID: PMC10785913.Peer-Reviewed Original ResearchConceptsDocument ontologyElectronic health recordsBag-of-words approachNatural language processing techniquesFree-text documentsLanguage processing techniquesClinical documentationLogical Observation IdentifiersText documentsStructured metadataWords approachComputational scalabilityMetadataHealth recordsEHR documentationElectronic health record fieldsProcessing techniquesOntologyDocumentsAutomated pipelineNLPScalabilityClinical careFrameworkLOINC
2023
FinFax: Fast Interpretation of Fax with NLP
Anjum O, Chen L, Denlinger R, Anam E, Dongsheng Y, Wooldridge C, Citardi M, Zhang J, Xu H, Jiang X. FinFax: Fast Interpretation of Fax with NLP. 2023, 1-2. DOI: 10.1145/3584371.3613019.Peer-Reviewed Original ResearchEnd systemCritical medical informationElectronic health record systemsHealth record systemsReal-life applicationsVital clinical dataFirst endManual processingInformation exchangeHealthcare organizationsOverall workflowHealth recordsMedical informationRecord systemWorkflowFinal outputFast interpretationFaxAcademic environmentInformationPertinent informationMultiple solutionsProcessingReal-life hospital settingsNLP
2022
Evaluation of mCODE Coverage in EHR: a Scoping Review of Cancer Natural Language Processing
Wang L, Fu S, Wen A, Ruan X, He H, Liu S, Moon S, Mai M, Riaz I, Wang N, Yang P, Xu H, Warner J, Liu H. Evaluation of mCODE Coverage in EHR: a Scoping Review of Cancer Natural Language Processing. 2022, 00: 517-518. DOI: 10.1109/ichi54592.2022.00094.Peer-Reviewed Original Research
2019
Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP
Soysal E, Warner J, Wang J, Jiang M, Harvey K, Jain S, Dong X, Song H, Siddhanamatha H, Wang L, Dai Q, Chen Q, Du X, Tao C, Yang P, Denny J, Liu H, Xu H. Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP. 2019, 264: 1041-1045. PMID: 31438083, PMCID: PMC7359882, DOI: 10.3233/shti190383.Peer-Reviewed Original ResearchConceptsElectronic health recordsNLP solutionNatural language processing technologyInformation extraction moduleLanguage processing technologyInformation extraction tasksUser-friendly interfaceBest F-measureInformation extractionExtraction moduleExtraction taskCustomizable modulesNLP systemsF-measureAcademic useHealth recordsComparable performanceProcessing technologyVanderbilt University Medical CenterModuleDiverse typesInformationNLPSubstantial effortSystem
2014
Open Source Clinical NLP - More than Any Single System.
Masanz J, Pakhomov S, Xu H, Wu S, Chute C, Liu H. Open Source Clinical NLP - More than Any Single System. AMIA Joint Summits On Translational Science Proceedings 2014, 2014: 76-82. PMID: 25954581, PMCID: PMC4419764.Peer-Reviewed Original ResearchClinical NLPNLP systemsNatural language processing toolsOpen source softwareLanguage processing toolsInformation technology practicesPluggable componentsSource softwareNLP softwareProcessing capabilitiesProcessing toolsResearch communityNLPCollaborative communitySingle systemSoftwareTechnology practicesNLP activityUIMAAnnotatorsSystemApacheOngoing activityFrameworkCapability
2006
Natural language processing and visualization in the molecular imaging domain
Tulipano P, Tao Y, Millar W, Zanzonico P, Kolbert K, Xu H, Yu H, Chen L, Lussier Y, Friedman C. Natural language processing and visualization in the molecular imaging domain. Journal Of Biomedical Informatics 2006, 40: 270-281. PMID: 17084109, DOI: 10.1016/j.jbi.2006.08.002.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineComputational BiologyDatabases, BibliographicDatabases, GeneticDiagnostic ImagingGenomicsHumansInformation Storage and RetrievalNatural Language ProcessingPhenotypeProgramming LanguagesSoftwareSystems IntegrationTerminology as TopicUser-Computer InterfaceVocabulary, ControlledConceptsImaging domainNatural language processing systemsNatural language processingLanguage processing systemJava viewerNLP systemsFormal evaluation studiesLanguage processingInformation resourcesProcessing systemMedical imagingIndex imagesSystem performanceBiological informationInformationImagesVisualizationBioMedLEEPerformanceNLPEvaluation studyDomainGenomics literatureSystemSimultaneous visualization