2021
LinkedImm: a linked data graph database for integrating immunological data
Bukhari SAC, Pawar S, Mandell J, Kleinstein SH, Cheung KH. LinkedImm: a linked data graph database for integrating immunological data. BMC Bioinformatics 2021, 22: 105. PMID: 34433410, PMCID: PMC8385794, DOI: 10.1186/s12859-021-04031-9.Peer-Reviewed Original ResearchConceptsGraph databaseGraph-based query languageVisual graph query interfacesNoSQL database technologyHeterogeneous biological dataWeb-based dashboardQuery interfaceQuery languageDatabase technologyGraph dataSQL databaseData retrievalData integrationMultiple data typesBiomedical domainNatural languageData typesUsersBiological dataMultiple sourcesScalable methodDatabaseLanguageMetadataSystems biology studies
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
2016
VDJML – tools for capturing the results of inferring immune receptor rearrangements
Toby I, Breden F, Buntzman A, Christley S, Corrie B, Fonner J, Gupta N, Hershberg U, Jordan C, Kim M, Kleinstein S, Marthandan N, Mock S, Monson N, Rounds W, Rojas M, Rosenfeld A, Rubelt F, Scarborough W, Scheuermann R, Scott J, Uduman M, Heiden J, Cowell L. VDJML – tools for capturing the results of inferring immune receptor rearrangements. The Journal Of Immunology 2016, 196: 209.24-209.24. DOI: 10.4049/jimmunol.196.supp.209.24.Peer-Reviewed Original ResearchFile formatOutput filesFile format standardsStandardized file formatDifferent file formatsStandardized formatApplication-agnostic mannerFormat standardsSoftware toolsCode contributionsCommand lineAnalysis applicationsImmune repertoire profilingAnalysis toolsDifferent labelsUsersFormatSoftwareFilesSuitePythonIgBLASTSharingToolWidespread use