2023
Mining of EHR for interface terminology concepts for annotating EHRs of COVID patients
Keloth V, Zhou S, Lindemann L, Zheng L, Elhanan G, Einstein A, Geller J, Perl Y. Mining of EHR for interface terminology concepts for annotating EHRs of COVID patients. BMC Medical Informatics And Decision Making 2023, 23: 40. PMID: 36829139, PMCID: PMC9951157, DOI: 10.1186/s12911-023-02136-0.Peer-Reviewed Original ResearchConceptsElectronic health recordsCoronavirus Infectious Disease OntologyGranular conceptsTextual dataInterface terminologyVolume of textual dataSNOMED CTLack of annotationsMining of electronic health recordsMachine learning modelsInfectious Disease OntologyTraining dataAutomatic annotationAutomatic extractionLearning modelsMining approachHold-out datasetElectronic health record dataCOVID-19 terminologyHealth recordsAnnotationOntologyDisease OntologyDatasetSNOMED
2021
Visual comprehension and orientation into the COVID-19 CIDO ontology
Zheng L, Perl Y, He Y, Ochs C, Geller J, Liu H, Keloth V. Visual comprehension and orientation into the COVID-19 CIDO ontology. Journal Of Biomedical Informatics 2021, 120: 103861. PMID: 34224898, PMCID: PMC8252699, DOI: 10.1016/j.jbi.2021.103861.Peer-Reviewed Original ResearchConceptsPartial-area taxonomyCoronavirus Infectious Disease OntologyCompact viewMedium sized ontologiesNames of nodesVisual patternsInfectious Disease OntologySummarization networkOntologyUsersVisual comprehensionDisease OntologyVisualizationNodesTaxonomyLayoutSummarizationGranularityNetworkCIDOConceptViews
2020
Outlier concepts auditing methodology for a large family of biomedical ontologies
Zheng L, Min H, Chen Y, Keloth V, Geller J, Perl Y, Hripcsak G. Outlier concepts auditing methodology for a large family of biomedical ontologies. BMC Medical Informatics And Decision Making 2020, 20: 296. PMID: 33319713, PMCID: PMC7737254, DOI: 10.1186/s12911-020-01311-x.Peer-Reviewed Original ResearchConceptsFamily of ontologiesSummarization networkMeta-ontologyQA techniquesPartial-area taxonomySets of conceptsSpecimen hierarchyScalabilityQA frameworkOntology hierarchyOntologySummarizationNetworkBioPortal ontologiesAudit methodologyQuality assuranceHierarchyNCBOBig pictureCollection of familiesGene hierarchySNOMEDMining Concepts for a COVID Interface Terminology for Annotation of EHRs
Keloth V, Zhou S, Lindemann L, Elhanan G, Einstein A, Geller J, Perl Y. Mining Concepts for a COVID Interface Terminology for Annotation of EHRs. 2020, 00: 3753-3760. DOI: 10.1109/bigdata50022.2020.9377981.Peer-Reviewed Original ResearchInterface terminologyDeluge of medical dataAnnotated clinical notesMachine learning techniquesConcept miningTraining dataClinical textHuge volumesLearning techniquesMining conceptsGranular conceptsMedical dataEHRInitial versionIncomplete dataAnnotationMiningCOVID-19 patientsHealthcare servicesConcatenationHealthcare deliveryDelugeOntologyMachineConcept
2018
How Sustainable are Biomedical Ontologies?
Geller J, Keloth V, Musen M. How Sustainable are Biomedical Ontologies? AMIA Annual Symposium Proceedings 2018, 2018: 470-479. PMID: 30815087, PMCID: PMC6371329.Peer-Reviewed Original ResearchExtended Analysis of Topological-Pattern-Based Ontology Enrichment
He Z, Keloth V, Chen Y, Geller J. Extended Analysis of Topological-Pattern-Based Ontology Enrichment. 2023 IEEE International Conference On Bioinformatics And Biomedicine (BIBM) 2018, 00: 1641-1648. PMID: 30854243, PMCID: PMC6402505, DOI: 10.1109/bibm.2018.8621564.Peer-Reviewed Original ResearchUnified Medical Language SystemTarget ontologyNational Cancer Institute ThesaurusMaintenance of biomedical ontologiesPairs of ontologiesMedical Language SystemHuman expertsCross-ontologyReference ontologyBiomedical ontologiesOntologyLanguage systemExpert resourcesHierarchical relationshipsTheoretical analysisApproximate locationTopological patternsThesaurusReference conceptTaskConceptClassificationMethodUnified