2019
A linked data graph approach to integration of immunological data
Bukhari SAC, Mandell J, Kleinstein SH, Cheung KH. A linked data graph approach to integration of immunological data. Bioinformatics And Biomedicine 2019, 00: 1742-1749. PMID: 34707915, PMCID: PMC8547546, DOI: 10.1109/bibm47256.2019.8982986.Peer-Reviewed Original ResearchGraph databaseDatabase technologyGraph-based query languageNatural language query interfaceNoSQL database technologyGraph-based databasesNeo4j graph databaseSQL database technologyHeterogeneous biological dataWeb-based dashboardQuery interfaceQuery languageData retrievalData integrationMultiple data typesBiological databasesData repositoryData typesResponse measurement dataGraph approachPathway dataData setsUsersBiological dataScalable method
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 ResearchConceptsData annotationBiomedical datasetsData management environmentData discoveryMetadata repositoryMetadata authoringData reuseEnd solutionMetadata templateData repositoryData entryRepositoryMetadataAnnotationDatasetComputational techniquesRetrievalExperimental datasetsProject consortiumStandard templateHuman Immunology Project ConsortiumAuthoringDifferent kindsDevelopersPossible refinements