Download - The Basics of VHA Data - Stanford Medicine · 3/12/18 6 •Additional documents that may be required: •Data Request Forms •Research Request Memo–Replaces the 9957 for ALLresearch

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TheBasicsofVHADataAccessing,Requesting,and

AnalyzingLauraA.Graham,PhD,MPH

HealthServicesResearchFellow,Ci2i,VAPaloAltoPostdoctoralFellow,SPIRE,StanfordUniversity

PriorSteps

• Beforerequestingdataaccess…

• Writeaclearprotocol• Knowyourstudyteam• GetVAAccess(Employed,WOC’ed)• GetIRBApproval!

ResearchIdea

Protocol

Funding?

IRBApplication

DUAs/DTAs

BeginResearch

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SeekingInformationonVAData?

• VHADataPortal• http://vaww.vhadataportal.med.va.gov/• GreatresourceforVHAdata

• VHADataArchitectureRepository• https://vaausdarmul81.aac.dva.va.gov/• DetaileddatadictionaryforCDWtables• SearchstringcanbeusefulforfindingdataburiedinCDWtables

SeekingInformationonVAData?

• VAInformaticsandComputingInfrastructure(VINCI)• https://vaww.vinci.med.va.gov/vincicentral/

• VAInformationResourceCenter(VIReC)• http://vaww.virec.research.va.gov/

• VAHealthEconomicsResearchCenter(HERC)• http://vaww.herc.research.va.gov/

• OfficeofPerformanceMeasurement(OPM)• https://vaww.car.rtp.med.va.gov/

• PlanningSystemSupportGroup(PSSG)• http://vaww.pssg.med.va.gov/

• Data.gov/CorporateDatabasesMonograph• www.data.gov

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ReadilyAvailableDataSources

• VHASupportServiceCenter• https://vssc.med.va.gov/• Facility-levelinformation

• BusinessOperations• ClinicalCare• Quality&Performance

• NationalCenterforVeteransAnalysisandStatistics• https://www.va.gov/vetdata/

DART

DataAccessRequestTracker

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RequestingVHADataAccess

• MostofyourdataaccessrequestswillbecoveredbytheDataAccessRequestTracker(DART)• https://dart.vha.med.va.gov/

• OtherdatasourcesexistandtheirrequestprocessescanbefoundintheVHADataPortal• http://vaww.vhadataportal.med.va.gov/

DataAccessRequestTracker(DART)

• Onlineworkflowapplication• DatarequestsandPreptoResearchRequests

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• DARTisyourstartingplaceforVINCIdataaccessamongothersources• AcquiresNationalDataService(NDS)approval• OnceapprovedanassignedVHAdatamanagerwillprovideaVINCIWorkspaceandaccesstodata• WillhelpyounavigateVINCI

VINCIhelpswithorangeboxes

• https://dart.vha.med.va.gov/

• CompleteanduploadtherequireddocumentsaslistedinDARTforthedatasource(s)ordatatool(s)selected.• Someofthefollowingdocumentswillberequired:

• ResearchProjectDocumentsandApprovals• Researchstudyprotocol• ResearchandDevelopmentCommitteeApprovalLetter(s)• InstitutionalReviewBoard(IRB)ApprovalLetter(s)• IRBApprovedHIPAAAuthorizationorWaiverofHIPAAAuthorization• IRBApprovedSampleInformedConsentorWaiverofInformedConsent


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• Additionaldocumentsthatmayberequired:• DataRequestForms

• ResearchRequestMemo – Replacesthe9957forALL researchrequestssubmittedthroughDART afterMarch25,2015

• RealSSNAccessRequest – RequiredforaccesstorealSSNs• CDWDomainCheckList – CDWdataonly• VitalStatusRulesofBehavior – VitalStatusFileonly• SpecialUserAccessRequestFormforResearchers – CAPRIandVistAWeb only• SurgeryDataResearchProposalTemplate – SurgicalQualityDataUseGroup(SQDUG)dataonly

• NationalSurgeryOffice(NSO)DataUseAgreementandSecurityInformation – SQDUGdataonly



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• Onceallrequireddocumentsareuploaded andtherequesthasbeensubmitted,itwillundergoaprivacyreview.

• Additionalreviewsarerequiredforthefollowing:• RequestsfordatawithrealSSNswillundergoreviewbytheOfficeofResearch&Development.

• RequestswillundergoasecurityreviewusingtheinformationprovidedintheResearchRequestMemo.



• WhendoIneedtorequestRealSSNs?

• You’replanningtousechartabstraction• You’relinkingtoanotherexistingdatasourcebySSN• You’replanningtousetheTIU(TextIntegrationUtilities)

• EverythingelseislinkedbyeitherSta3n/PatientSID orSCRSSN andyouwillreceiveacrosswalkfileonceyourrequestisapproved

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• AfterdataaccessapprovalaVINCIDataManagercanhelpwiththefollowing:• Cohortselection• DataExtraction• Formatting,Indexing,andSecurity

OtherDataAccessExamples

• OfficeofReportingAnalyticsPerformanceImprovementandDeployment(RAPID)• DUAForms

• ProjectInformationSheet• PersonalAgreementStatement• DataAccessList

• StudyProtocol• IRBApproval• DataRequestSpecifications

• [email protected]

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VINCITheVAInformaticsandComputingInfrastructure

VINCIIntroduction

• Web-basedplatformforaccessingandanalyzingdatawithavarietyoftools• ProvidesconsultationservicesforIRBResearchfortheentirelife-cycleofaresearchproject• https://vaww.vinci.med.va.gov/vincicentral/

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VINCIIntroduction

• https://vaww.vinci.med.va.gov/vincicentral/

• 105high-performanceserversand1.5petabytesofdatastorage• 450+newprojects– 17%increaseYOY• Provideddatato840+projects• VINCIDataAnalyststouchabout50projects/week• Structure

• Windows2012R2Workspace• SQLServers(Currently3)

• RB01:vhacdwdbs01.vha.med.va.gov• RB02:vhacdwdbs02.vha.med.va.gov• RB03:vhacdwdbs03.vha.med.va.gov

VINCIUse

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VINCIUserGuides

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VINCIStandardWorkspaceApplications

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• IconsontheStandardWorkspacelinktoremotedesktopservers• Yourlog-inandpasswordarethesameasforyourVAcomputer(i.e.vhapal …)• Theoveralldesktopapplicationhaslimitedsoftwareavailability.• Logintoeachapplicationseparately• Eachwillbeaseparatedesktop/server

• TheSAS9.xiconisagoodplacetostart.

VINCIFolderSetUp

• Sameasonadesktop• HardDiskDrives(K,L,M,N,T,S,U,V,X)• NetworkDrives

• P:/drive(Projects)• O:/drive(Projects2)• H:/drive

• AllprojectfoldersaretypicallyfoundintheP:/drive• H:/isyourpersonalfolder• Allprojectfoldershaveasub-foldernamedUploads whereuploadedinformationisincluded

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VINCIFolderSetUp

VINCI– MoreInformation

• MoreinformationonaccessingandusingtheVINCIWorkspacearefoundintheVINCIWorkspaceUserGuide

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SQLServerManagementStudio

ViewYourData

SQLServerManagementStudio

• 2017version• MethodforaccessingandviewingCDWdomaintableswithSQLcode• Canalsobeusedtopulldataina.txtformatifneeded• RequiressomeinitialsetuptolinktoserversandsomeSQLknowledgebutalsohaspoint-and-clickoptions thatmakeiteasytouse

• Thebestplacetostartlookingatdatayou’vebeengivenaccesstoforyourstudy

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SQLServerManagementStudioSetUp• VINCIDatabaseUserGuide• Section4.2.1(pages3-4)providesdetailedinformationonSQLserversetup

DefaultSettingsToUse

ServerType: DatabaseEngine

ServerName: .vha.med.va.gov

Authentication: WindowsAuthentication

SQLServerManagementStudioDataAccess• VINCIDatabaseUserGuide• Section4.2.2(pages4-7)providesdetailedinformationonaccessingdatabases

• Overview• Databases>CDWWork containsyourdimensiontables• Databases>ORD_XXXX>Views containsyourSQLdatatables• Right-clickand“SelectTop1000Rows”foreasyviewingofadatasource

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SQLServerManagementStudioDataPulls• NotasefficientasaSASpullbutcanbedone

• First,setupyourquery.YourinitialrunswillbeoutputtoGrid.

• Onceyourqueryissetup• Use“Query>ResultsTo”tochangeto“ResultstoFile”• Then“Query>QueryOptions…”tosetupyourfilebutnavigatingthrough“Results>Text”

ApplicationsforAnalysis

AnalyzeYourData

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VINCISAS

• LotsofUserGuidesforreference• Thiscourseisonlyanintrobutthesewillansweryourmoreadvancedquestions.

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VINCISAS

• SeveralversionsofSASareavailableforuse.• SAS9.2• SAS9.4• SASEnterpriseGuide7.1

• Allofferdifferentcapabilitiessocheckwithallofthem

VINCISAS

• “Grid”referstotheLinuxoperatingsystemwhereSASEnterpriseGuide7.1 runs• Youwillneedaslightlydifferentlibname reference:“/data/dart/2014/ORD_Smith_201401001D/“

• YouwillalsoneedtouseWINSCPfordatatransferandaPIV-exemptiontoaccesstheGrid

• Checkout“Grid– WheretoBegin?”formoreinformation• SAS9.2and9.4 arenotonthegridandsometimeseasiertoworkfrom.• Plus,SAS9.2istheonlyprogramwithPROCTRAJ!

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VINCISASDataPulls

• ItendtouseSAS9.2orSAS9.4totunnelintotheCDWandpullmydatadirectlyintoSAS.

• Thisrequiresthefollowingcode:

• TheCatalogischangedtoreferenceyourprojectfolder.• “Datasource”mayalsoneedtobechangedbasedonyourprojectserver.• Schemawillchangebasedonwhatviewyouarelookingat(SRC,Dim,…)

VINCISASDataPulls

• PROCSQListypicallyhowIpullandmergethedatainSAS9.4• IinitiallysetupthetestdatapullsinSQLManagementStudiousingapullofthetop100 totestthequeries• OncemySQLcodelooksIgoodthenImoveittoSAS,removethebrackets,updatethelibnames andrun.

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VINCISASDataPulls

• ThiscangetcomplicatedwithmultiplejoinsandWherestatements.

VINCISASDataPulls

• SQLpass-throughlanguageisalsoaquickwayoftunnelingintotheSQLtablesandpullingoutdata.

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VINCIEnterpriseGuide7.1

• VINCISAS9.4and9.2arelimitedinthetypesofanalysesthatcanbedone

• VINCIEnterpriseGuideofferseverythingandisbyfarthemostcapableoftheSASproductsbutyouhavetosetuplinkstotheGridandmoveyourfilestotheLinuxsystem

• Itendtodomostofmydatamanagementandcleaningin9.4andthenswitchtheanalyticdatasettoLinuxformyanalyses


• ThefirststeptousingEnterpriseGuide7.1istocheckyourLinuxsystemregistrationbysettingupWinSCP• OncesetupWinSCP isyourmethodformovingfilesfromPCtoLinux• ThiscanbedonebyfollowingtheinstructionsinUsingEnterpriseGuidewiththeGrid

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WinSCP


• TouseSASEnterpriseGuide7.1youwillneedtosetupyourconnection

• ThiscanbedonebyfollowingtheinstructionsinUsingEnterpriseGuidewiththeGrid

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Policies

ProtectYourData

PoliciesforElectronicData

• VAHandbook6500• DefinitionsandguidancefortheVHA

• KeyPoints• USBdrivesareforbidden• DonotstoresensitiveinformationonaHardDrive(C:/Drive).Trynottostoreanythingonaharddrive.

• Sensitiveinformationcanneverbetransported,accessed,processedorotherwiseusedoffsite.DON’TEMAILDATA!

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TypesofData

1. IndividuallyIdentifiableHealthInformation2. ProtectedHealthInformation(PHI)3. PersonallyIdentifiableInformation(PII)4. VASensitiveInformation/Data

• VHAHandbook6500 providesguidanceondefinitionsandmanagement

DisposalofData

• GovernedbytheVHARecordControlSchedule (RCS10-1)

• Currentguidance(Item8300.6,PageIII-8-6)• Temporary;cutoffattheendofthefiscalyearaftercompletionoftheresearchproject.• Destroy6yearsaftercutoff,mayretainlongerifrequiredbyotherFederalregulations.(DAA-0015-2015-0004,item0032)

• IftheinvestigatorleavesVA,allresearchrecordsareretainedbytheVAfacilitywheretheresearchwasconducted.

• IfthegrantisongoingandtheinvestigatorleavesoneVAfacilitytogotoanotherVAfacility,theinvestigatormustobtainapprovalforacopyofrelevantmaterialstobeprovidedtothenewVAfacility'sresearchoffice.

• Theinvestigatorisnotthegrantee,nordoestheinvestigatorownthedata.

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FunThingstoDo

FullOrganizationalView

• >9MillionEnrolledPatients

• 170VAMedicalCenters(141withSurgicalCapacity)

• 1,063OutpatientCenters

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LongitudinalData

• AllvitalsandlaboratoryvaluescollectedintheVAareeasilyaccessible

• Pharmacyprescriptions–inpatient,outpatient,andevenevidenceofnon-VAprescriptionsareavailable

JAMA Surg. 2014;149(11):1113-1120. doi:10.1001/jamasurg.2014.2044

NaturalLanguageProcessingCapabilities

• Linguistic-computerscienceresearch• Abilityofacomputerprogramtounderstandhumanlanguageasitiswritten infree-textofclinicalnotes• SeveralVAtoolstoworkwith

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Thankyou!