Formalization, Annotation and Analysis of Diverse Drug and Probe Screening Assay Datasets Using the BioAssay Ontology (BAO) 英文参考文献.docVIP

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Formalization, Annotation and Analysis of Diverse Drug and Probe Screening Assay Datasets Using the BioAssay Ontology (BAO) 英文参考文献.doc

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Formalization, Annotation and Analysis of Diverse Drug and Probe Screening Assay Datasets Using the BioAssay Ontology (BAO) 英文参考文献

Formalization,AnnotationandAnalysisofDiverseDrug andProbeScreeningAssayDatasetsUsingtheBioAssay Ontology(BAO) UmaD.Vempati1,MagdalenaJ.Przydzial1,CatyChung1,SamindaAbeyruwan2,AhsanMir1, KunieSakurai1,UbboVisser2,VanceP.Lemmon3,StephanC.Schu¨rer1,4* 1CenterforComputationalScience,UniversityofMiami,Miami,Florida,UnitedStatesofAmerica,2DepartmentofComputerScience,UniversityofMiami,Miami,Florida, United States of America, 3The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami, Miami, Florida, United States of America, 4DepartmentofMolecularandCellularPharmacology,UniversityofMiami,Miami,Florida,UnitedStatesofAmerica Abstract Hugeamountsofhigh-throughputscreening(HTS)dataforprobeanddrugdevelopmentprojectsarebeinggeneratedin thepharmaceutical industryandmorerecentlyin thepublicsector. Theresultingexperimental datasetsareincreasingly beingdisseminatedviapublicallyaccessiblerepositories.However,existingrepositorieslacksufficientmetadatatodescribe theexperimentsandareoftendifficulttonavigatebynon-experts.Thelackofstandardizeddescriptionsandsemanticsof biologicalassaysandscreeningresultshindertargeteddataretrieval,integration,aggregation,andanalysesacrossdifferent HTSdatasets,forexampletoinfermechanismsofactionofsmallmoleculeperturbagens.Toaddresstheselimitations,we createdtheBioAssayOntology(BAO).BAOhasbeendevelopedwithafocusondataintegrationandanalysisenablingthe classification of assays and screening results by concepts that relate to format, assay design, technology, target, and endpoint.Previously,wereportedonthehigher-leveldesignofBAOandonthesemanticqueryingcapabilitiesofferedby theontology-indexed triplestoreofHTSdata.Here, wereportonourdetaileddesign,annotationpipeline,substantially enlargedannotationknowledgebase,andanalysisresults.WeusedBAOtoannotateassaysfromthelargestpublicHTSdata repository,PubChem,anddemonstrateitsutilitytocategorizeandanalyzediverseHTSresultsfromnumerousexperiments. BAO is publically available fro