2024
Extracting Systemic Anticancer Therapy and Response Information From Clinical Notes Following the RECIST Definition
Zuo X, Kumar A, Shen S, Li J, Cong G, Jin E, Chen Q, Warner J, Yang P, Xu H. Extracting Systemic Anticancer Therapy and Response Information From Clinical Notes Following the RECIST Definition. JCO Clinical Cancer Informatics 2024, 8: e2300166. PMID: 38885475, DOI: 10.1200/cci.23.00166.Peer-Reviewed Original ResearchConceptsNatural language processingDomain-specific language modelsNatural language processing systemsInformation extraction systemRule-based moduleNarrative clinical textsNLP tasksEntity recognitionText normalizationAssertion classificationLanguage modelInformation extractionClinical textElectronic health recordsLearning-basedClinical notesLanguage processingTest setSystem performanceHealth recordsResponse extractionTime-consumingAnticancer therapyInformationAssessment information
2021
OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers
Zhang Y, Yao X, Zhou H, Wu X, Tian J, Zeng J, Yan L, Duan C, Liu H, Li H, Chen K, Hu Z, Ye Z, Xu H. OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers. Nucleic Acids Research 2021, 50: d1340-d1347. PMID: 34554251, PMCID: PMC8728274, DOI: 10.1093/nar/gkab851.Peer-Reviewed Original ResearchConceptsAlternative splicingCancer-specific splicing eventsDifferential alternative splicingHuman cancersTCGA tumor samplesSplicing differencesSplicing eventsProtein complexityAdjacent normal samplesSplicingGene expressionSplicing dataNormal samplesAbnormal splicingIntegrative viewMRNA levelsDifferential analysisTumor samplesTranscripts
2020
Efficient and Accurate Extracting of Unstructured EHRs on Cancer Therapy Responses for the Development of RECIST Natural Language Processing Tools: Part I, the Corpus
Li Y, Luo Y, Wampfler J, Rubinstein S, Tiryaki F, Ashok K, Warner J, Xu H, Yang P. Efficient and Accurate Extracting of Unstructured EHRs on Cancer Therapy Responses for the Development of RECIST Natural Language Processing Tools: Part I, the Corpus. JCO Clinical Cancer Informatics 2020, 4: cci.19.00147. PMID: 32364754, PMCID: PMC7265793, DOI: 10.1200/cci.19.00147.Peer-Reviewed Original ResearchConceptsNatural language processing toolsElectronic health recordsLanguage processing toolsGold standard dataUnstructured electronic health recordsProcessing toolsAmount of dataClinical notesStandard dataMayo Clinic electronic health recordsClinic's electronic health recordEnvironment toolsAccurate annotationHealth recordsInformatics toolsEffective analysisData setsTextual sourcesCorpusToolInformationData extractionSetExtractingAnnotationAchievability to Extract Specific Date Information for Cancer Research.
Wang L, Wampfler J, Dispenzieri A, Xu H, Yang P, Liu H. Achievability to Extract Specific Date Information for Cancer Research. AMIA Annual Symposium Proceedings 2020, 2019: 893-902. PMID: 32308886, PMCID: PMC7153063.Peer-Reviewed Original Research