2020
A structured model for immune exposures
Vita R, Overton JA, Dunn P, Cheung KH, Kleinstein SH, Sette A, Peters B. A structured model for immune exposures. Database 2020, 2020: baaa016. PMID: 32283555, PMCID: PMC7153954, DOI: 10.1093/database/baaa016.Peer-Reviewed Original ResearchMeSH KeywordsAntibodiesAntigensBiological OntologiesComputational BiologyData CurationDatabases, FactualEpitopesHumansImmune SystemImmune System DiseasesConceptsImmune exposure
2019
Reporting and connecting cell type names and gating definitions through ontologies
Overton JA, Vita R, Dunn P, Burel JG, Bukhari SAC, Cheung KH, Kleinstein SH, Diehl AD, Peters B. Reporting and connecting cell type names and gating definitions through ontologies. BMC Bioinformatics 2019, 20: 182. PMID: 31272390, PMCID: PMC6509839, DOI: 10.1186/s12859-019-2725-5.Peer-Reviewed Original Research
2018
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata
Bukhari SAC, Martínez-Romero M, O’ Connor M, Egyedi AL, Willrett D, Graybeal J, Musen MA, Cheung KH, Kleinstein SH. CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. BMC Bioinformatics 2018, 19: 268. PMID: 30012108, PMCID: PMC6048706, DOI: 10.1186/s12859-018-2247-6.Peer-Reviewed Original ResearchConceptsMetadata entriesBrowser extensionWeb formsData repositoryOntology-based metadataWeb page contentBiomedical data repositoriesWeb-based interfacePage contentPublic data repositoriesRelevant ontologiesHTML formatSource datasetIndividual repositoriesNCBO BioPortalCollected metadataExperimental metadataScientific metadataMetadataOndemandPre-defined listOntologyRepositoryInput fieldDataset
2015
The center for expanded data annotation and retrieval
Musen MA, Bean CA, Cheung KH, Dumontier M, Durante KA, Gevaert O, Gonzalez-Beltran A, Khatri P, Kleinstein SH, O’Connor M, Pouliot Y, Rocca-Serra P, Sansone SA, Wiser JA, team A. The center for expanded data annotation and retrieval. Journal Of The American Medical Informatics Association 2015, 22: 1148-1152. PMID: 26112029, PMCID: PMC5009916, DOI: 10.1093/jamia/ocv048.Peer-Reviewed Original ResearchMeSH KeywordsBiological OntologiesBiomedical ResearchData MiningDatasets as TopicHumansInformation Storage and RetrievalUnited StatesConceptsData annotationBiomedical datasetsData management environmentData discoveryMetadata repositoryMetadata authoringData reuseEnd solutionMetadata templateData repositoryData entryRepositoryMetadataAnnotationDatasetComputational techniquesRetrievalExperimental datasetsProject consortiumStandard templateHuman Immunology Project ConsortiumAuthoringDifferent kindsDevelopersPossible refinements