the bdds platform for big biomedical data...
TRANSCRIPT
The BDDS Platform for Big Biomedical Data Management and Analysis: Discovering the role of Amyloid Deposition in Neurodegenerative Diseases
Ravi K Madduri, Michael D’Arcy, Kyle Chard, Alexis Rodriguez, Judy Pa, Naveen Ashish, Ben Heavner, Gustavo Glusman, Ivo Dinov, John Van Horn, Eric Deutsch, Nathan Price, Leroy Hood, Carl Kesselman, Ian Foster, Joseph Ames, Arthur Toga
University of Chicago, University of Southern California, Institute for Systems Biology, University of Michigan
Abstract
Approach
The BDDS Platform Analyzing role of Amyloid Burden
Discussion & Conclusions
Bibliography
Objective:Investigateiftherearecommonalitiesinpatternsofamyloiddeposition inindividualswithAlzheimer’sDiseaseorParkinson’sDiseasethatidentifythoseindividualswithoratriskforcognitivedysfunctionApproach:Wecreatedaplatform forintegrationofmulti-omic data,facilitatedatadiscovery,cohortcreation, enablerapid,scalableandreproducible analysisandfinallypublishresults
Weemployedasystematic,reproducibleapproachthatleveragedexistingcapabilitiesforunderstandingcommonalitiesinamyloiddepositionthatincludedthefollowingstagesandchallenges
1.DataIngest- ERMRest• Phenotypic,Genotypicand
Imagingdatasets• Multiplerepositories• DataUsageAgreements• Automateddatacleanupand
ingest
2.DataQueryandExchange- BagIt• ERMRest provideshigh-levelAPI
forquery• AdoptedtheBagIt specification
tocreatedatabags• EnhancedBagIt tosupportbig
biomedicaldata3.DataAnalysis– PipelineandGlobusGenomics• LONIPipelinerunstheanalysis
ontheamyloidPETandMRIimagesandoutputsamyloidindexvalues(SUVR:standarduptakevalueratio)foreachbrainregion,foreachsubjectusingcomputationalresourcesatUSC
• GenomicsanalysisusingGlobusGenomicsontheAmazoncloud
• Leverageselasticprovisioner thatoptimizesperformanceandcosts
4.DataPublicationandIntegration– GlobusPublicationandERMRest• Resultsfromanalysisare
integratedwithERMRest• ResultsarepublishedinGlobus
Publicationservicewithappropriatemetadata
• Multi-omic data• Multipledistributedrepositories• Data usage agreements• Data cleanup and integration
DataIngest
• Easy tofinddata• Enable creation ofpatient cohorts• Send data foranalysis
DataQueryandExchange
•Multipleanalysisplatforms• Ease ofuse• Scale
DataAnalysis
• Enable discovery• End-to-end data view
DataPublication
andIntegration
Images f r om Alzheim er 's andPar kinson's
1. TheBagIt FilePackagingFormat(V0.97)availableat:http://tools.ietf.org/html/draft-kunze-bagit-11
2. Minids:http://minid.bd2k.org
SUVR values forcortical gray matterregions of interestoverlaid onas tructural MRI for as inglesubject
Exom esandwholegenom es f r om Alzheim er 's andPar kinson'sPhenot ypic dat a
• Wecreatedapowerfulplatformbyintegratingseveralexistingservicesandcapabilities
• PlatformdevelopmentresultedinadoptingandextendingBagIt formatforbiomedicalbigdata
• FutureworkincludesapplyingtheplatformforanalyzingAlzheimer’sdata
• ReferenceimplementationoftheNIHCommons
ark:/88120/r83w2c