LabVantage-Reports External V2 - University of Chicago · 2017-08-01 · IRB protocol “Test123”...

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LabVantage User Manual: Reporting Features • Sample Family • Sample Lifecycle • Searching & Viewing Data • Creating Reports 1 Disclaimer: Printed copies are not the official document. Please see the online PDF file for the most up-to-date version. http://htrc.uchicago.edu 8/1/17

Transcript of LabVantage-Reports External V2 - University of Chicago · 2017-08-01 · IRB protocol “Test123”...

Page 1: LabVantage-Reports External V2 - University of Chicago · 2017-08-01 · IRB protocol “Test123” between the dates of 4/1/2015 -9/21/2015 • Select New AdHocQuery and select the

LabVantage UserManual:ReportingFeatures• SampleFamily• SampleLifecycle• Searching&ViewingData• CreatingReports

1Disclaimer:Printedcopiesarenottheofficialdocument.PleaseseetheonlinePDFfileforthemostup-to-dateversion.http://htrc.uchicago.edu 8/1/17

Page 2: LabVantage-Reports External V2 - University of Chicago · 2017-08-01 · IRB protocol “Test123” between the dates of 4/1/2015 -9/21/2015 • Select New AdHocQuery and select the

BringsyoubacktothispageLogoff

Changepassword

Clickonanyofthetramstops toaccess

thatpage

ThePI/RADashboardprovidesyouwithanoverviewofyourIRB

protocols2

NavigatingTheDatabase

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• LabVantage usestheconceptofasamplefamilytoorganizespecimensandsamples.Asamplefamilyconsistsofaparentsample(thisisthespecimen,e.g.,wholebloodortonsil)anditschildsamples(thesearethesamplesthatcamefromtheparent,e.g.,plasmaorOCTtumor)

• Youcantellwhichsamplesareparentsbylookingforthebeakericon:• Hint:parentsampleswillhaveastatusofdisposedandadispositionof

consumed

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ParentSample

ChildSamples

UnderstandingTheSampleFamily

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• IfyouwouldliketoviewfurtherinformationontheSampleFamily,clickontheboxnexttothesampleandselectSampleNavigator

• FromhereyouviewtheSampleDetailReportorexpandthefamilytree

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UnderstandingTheSampleFamily

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• Thestatusofasample,incombinationwithdispositionandcustodialdomain,explainswherethesampleisinthesamplelifecycle

• ThebelowchartwillhelpyouunderstandifthesampleisstoredintheHTRC,hasbeenpickedupandisnolongerintheHTRC’sstorage,orifasamplewasnotbankedduetoadverseconditions

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Status Disposition CustodialDomain MeaningInCirculation n/a HTRC Storedinbiobank

InCirculation n/a Transit Samplewaspreviouslywithdrawnfromthebiobank

3rd PartyTransfer n/a HTRC Samplewaspickedupsameday(ie.freshtissuepickedupsameday)

InPrep n/a HTRC Sampleisbeingprocessedandisnotreadytobedispersed/stored

Disposed Rejected HTRC Thisisasamplethatwascreatedautomaticallybythesoftwareandtherewasnotenoughbiospecimentofullfill it

Disposed SpecificReason HTRC Thesearesamplesthatwerenotbankedforspecificreasons,like"entirelysubmittedfordiagnostics”

Disposed Consumed HTRC Thisisaparentsamplethatwasconsumedinordertocreatechildsamples

UnderstandingSampleLifecycle

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• Nowthatyouunderstandtheconceptofthesamplefamilyandthesamplelifecycle,itistimetolearnhowtoviewdataandcreatereports

• TherearemanywaystoviewyourdatawithinLabVantage.TheeasiestwaytoseeaoverviewofyourdataistoutilizethePI/RADashboard

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• Youcanclickonthesliceofthepiegraphyou’reinterestedintoviewallofthedataassociatedwiththatprotocol

• Youcanalsoclickonthebargraphstoseespecificdataonsampletypes

AccessingData- Dashboard

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• Alternately,ifyouarelookingforspecificdataormorecomplexsearchingability,gototheSamplesTramstop

• Fromthispage,youcaneitherdoaquicksearchusingtheSearchByQueryoptions

• OryoucandoamorecomplexsearchbyusingtheNewAdhoc Queryfeature

• TheSearchByQueryoptionworkswellforquickandsimplesearches,likelookingforallsamplesfromapatientwithaspecificMRNorlookingforallsamplesbankedunderaspecificIRBprotocolnumber

• TheAdhoc Queryoptionworkswellformorecomplicatedsearches,likesearchingforallDNAsamplescollectedforaspecificprotocolthatwerepreviouslywithdrawn

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SearchingandViewingData

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UsingSearchByQueryOption• Let’ssayyouwanttoviewall

samplescollectedforaspecificpatient:– “JoeTest”– MRN=45689996

• SelecttheSearchByQueryOptionforMRN

• Type45689996intothesearchfieldandclickoktoviewthesearchresults

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SearchingandViewingData:SearchbyQuery

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• Herearethesearchresults:

• TrytochangetheGroupByoptiontoNone.Thiswillchangetheorderinwhichyoursamplesaredisplayed.Now,youshouldbeabletoviewaparentsamplewithitschildrentogether

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SearchingandViewingData:SearchbyQuery

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• Oursearchresultsshowthattherewere2parentsamplesbankedforJoeTest:

• Thefirstparentsampleisawholebloodsamplethathas3children,2plasmasamplesand1PBMCsample

• Thesecondparentsampleisatissuesamplethatwasnotbanked,withthereasonbeing“Other.”Inthiscase,youwillneedtoviewthesampledetailstoseethenotesinthecommentstab.Todothis,clickontheboxnexttothesample,selectview,andthenclickonthecommentstab

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SearchingandViewingData:SearchbyQuery

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• YoucanexporttheinformationdisplayedfromthesearchbyclickingeitherViewasPDForViewasExcel

• Youcanclickonthehyperlinkstoviewadditionalinformation

**Rememberthatparentsampleswillhavethebeakericon

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SearchingandViewingData:SearchbyQuery

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• Ifyouclickonthesamplenumberhyperlink,itwillopenupthesampledetails• Herearethedetailsforaparentspecimen,S091500009• YoucanclickontheSampleDetailReport,forevenmoredetails

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SearchingandViewingData:SearchbyQuery

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• Herearesomeofthemostutilizedsearchbyqueryelements:– ByMRN

• SearchbyMRN

– ByLastName• Searchbylastname

– ByProtocol• SearchbyIRBprotocolnumber

– ByProtocolandSampleType• SearchbyIRBprotocolnumberandsampletype

– PairedSamplesbyProtocol• Searchforpairedsamples(e.g.,tumorandnormalfromsameparent

sample)collectedunderaspecificIRBprotocol

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SearchingandViewingData:SearchbyQuery

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UsingAdHoc QueryOption• Adhoc QueriesworkbetterthanSearchByQueriesformorecomplicatedsearches• Let’ssayyouwanttoviewallsamplesthatwerecollectedfortheIRBprotocol“Test123”

betweenthedatesof4/1/2015- 9/21/2015• SelectNewAdHoc Queryandselectthesearchcriteriafromtheleftsideofthe

screenbyclickingontheicon• Important!Usethemagnifyingglassicontolookupdataelementsinsteadoftypinginto

thefield• Forthissearch,youwouldcreateanadhoc querylikethis:

Sinceyouwanttolookforsamplesthatareintheprotocol“Test123”and werereceivedbetween4/1/2015-9-21-2015,youshouldselectMeetALLoftheCriteria

Youwouldincludeprotocolandreceiveddate(usethereceiveddatefromthe

samplefamilynode)inthecriteriagroup

SearchingandViewingData:AdHocQuery

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• Onceyou’vecreatedyourAdHoc query,hitsearchtoviewresults• SelectspecificsamplesorallandexportthispageasaPDFortoExcel

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SearchingandViewingData:AdHocQuery

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UsingAdHoc QueryOptionwithmoredetails• Let’ssayyouwanttoviewallDNAandPBMCsamplesthatwerecollectedforthe

IRBprotocol“Test123”betweenthedatesof4/1/2015- 9/21/2015• SelectNewAdHoc Queryandselectthesearchcriteriafromtheleftside

ofthescreenbyclickingontheicon• Forthissearch,youwouldcreateanadhoc querylikethis:

Youwillneed2CriteriaGroupsforthissearch.UsetheNewCriteriaGroupbuttontoadd

CriteriaGroups

YourfirstCriteriaGroupwilllookforPMBCsamplesORDNAsamples.UseMeetANY

oftheCriteriaforthisCriteriaGroup

YoursecondCriteriaGroupwilllookfortheprotocol“Test123”ANDthedate

range.UseMeetALLoftheCriteriaforthisCriteriaGroup

Lastly,selectMeetALLoftheCriteriaGroups– thismeansthatALLofthecriteriafromtheCriteriaGroupsmustbemet

SearchingandViewingData:AdHocQuery

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• Onceyou’vecreatedyourAdHoc query,hitsearchtoviewresults• SelectspecificsamplesorallandexportthispageasaPDFortoExcel

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SearchingandViewingData:AdHocQuery

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SearchingandViewingData:AdHocQueryDataElementDictionaryPart1

AdHoc Search AdHoc SearchDescription BFExample TissueExampleSample SampleNumber S031606245 S031606247SampleType SampleType(child) DNA OCTDiseasedSampletypeDescription SampleType(child) DNA OCTDiseasedSampleFamily SampleFamilyID# SF-160325-00013 SF-160325-00014 StudySite StudySiteID# SS-00001279 SS-00001279StudysiteDescription StudySiteDesc.(WhereSpecimenWasProcessed) _P524 _P524CollectionDate SpecimenReceivedDate/Time 3/2/1610:25AM 3/25/1612:39PM RecievedDate DateSamplewasenteredintoLVbyHTRC 3/25/1612:26PM 3/25/1612:45PM Subject SubjectID# ST-00076083 ST-00076083BirthDate DOB 5/26/8112:00AM 5/26/8112:00AM GenderFlag Gender(MORFORU) M MMRN# MRN# 666666666666666 666666666666666Race Race WhiteorCaucasian. WhiteorCaucasian.Ethnicity Ethnicity NotHispanic/NotLatino NotHispanic/NotLatino

FirstName FirstName Testing TestingMiddleName MiddleName Nick NickLastName LastName Tester1 Tester1Disease DiseaseID# DS-00000002Tissue TissueOnly:TissueID# TS-00000110TissueDescription TissueDescription ColonInitialmass TissueParentSpecimenMass 1.0000000000InitialmassUnits TissueParentSpecimenMassUnit gInitialvolume BFParentSpecimenVolume 4.0000000000InitialvolumeUnits BFParentSpecimenVolumeUnit mlParticipant ParticipantID# P-00058724 P-00058724Externalparticipant ExternalParticipantID ExternalIDTest123 ExternalIDTest123ParticipantStatus ParticipantStatus Enrolled EnrolledEnrollDate ParticipantEnrollDate 10/6/1512:00AM 10/6/1512:00AM CompletedDate ParticipantCompletedDateWithdrawalDate ParticipantWithdrawalDateHeight TissueChildSampleHeight 0.5000000000Length TissueChildSampleLength 0.5000000000Width TissueChildSampleWidth 0.5000000000DimensionUnit TissueChildSampleDimensionUnit cmParticipantConsented ParticipantConsented(YorN) Y YSurgeryProcessTime TissueOnly:SurgerytoProcessTime 0-30MinutesActualCollectionDate&Time BFOnly:ActualCollection(DrawDate/Time) 3/1/1612:53PM

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SearchingandViewingData:AdHocQueryDataElementDictionaryPart2

AdHoc Search AdHocSearchDescription BFExample TissueExampleProcessedDate BFOnly:ProcessingDate/Time 3/2/1611:02AM SurgicalMethods TissueOnly:SurgicalMethod TotalColectomyConfirmedBy ConfirmedBy HTRC HTRCSysuserDescription SysuserDescription HTRCUserID HTRCUserIDDisabledFlag DisabledFlag N NEmail Email [email protected] [email protected] Defaultdepartment HTRC HTRCConfirmedDate DateSamplewasconfirmedinLVbyHTRC 3/25/1612:00AM 3/25/1612:00AM Protocol Protocol Test2015 Test2015StudyDescription StudyDescription IRBProtocolTemplate IRBProtocolTemplateDelinkableFlag DelinkableFlag(YorN) N NDuration DurationofProtocol 369 369UnitsofMeasurement DurationofProtocolUnits Years YearsAnticipatedStartDate AnticipatedStartDateofProtocol 7/31/1512:00AM 7/31/1512:00AM PIUser PIUser TestPI TestPIStorageStatus StorageStatusofSample InCirculation InCirculationStoragedisposalStatus StoragedisposalStatusIsitanExternallyprocessedSample? ExternallyProecessedSample(YorBlank) ySurgicalMethod surgicalmethodSurgicalPathologyNumber SurgicalPathologyNumber S-13123456 ParentSampleTypeID ParentSampleType(DRLOOKINTOTHIS) WholeBlood TissueSampletypeDescription ParentSampleType WholeBlood TissueNotes n/a ActiveFlag ActiveFlag Y YCustodialDomain CustodialDomain HTRC HTRCContainerType ParentSampleContainerType(ielavendertube)CurrentLocation CurrentStorageLocation /B031600052/A2 /B031600052/A3 Custodian Custodian drufo drufoQuantity CurrentSampleQuantity(VolumeorMass) 0.5000000000 0.5000000000ReservedLocation ReservedLocationSampleType Sampletype(child) DNA OCTDiseased260/280 Attribute- 260/280 2CellConcentration Attribute- cellconcentration 4CellViability Attribute- cellviability 5DNAConcentration Attribute- DNAconcentration 3OD260 Attribute- OD260 1SpecificTissueLocation Attribute- specifictissuelocation SpecificColonLocationBreast-ER(var:Breast-ERdataset:1)Breast-ER(Standard)rep:1 TissueOnly:TestResults PositiveBreast-HER2(var:Breast-HER2dataset:1)Breast-HER2(Standard)rep:1 TissueOnly:TestResults NegativeBreast-PR(var:Breast-PRdataset:1)Breast-PR(Standard)rep:1 TissueOnly:TestResults Negative

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• YounowhavetheskillstouseanAdhoc QuerytosearchfordatawithinLabVantage

• Next,youwilllearnhowtoutilizetheAdhoc Querytocreatecustomizedreports

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CreatingReports

Page 21: LabVantage-Reports External V2 - University of Chicago · 2017-08-01 · IRB protocol “Test123” between the dates of 4/1/2015 -9/21/2015 • Select New AdHocQuery and select the

UsingAdHoc Querytocreateareport

• GototheAdhoc QueryBiobanking LIMSpage

• Important!YoumustperformtheAdhoc Queryfromthistramstop inordertocreateareport.AccessingtheAdhoc QueryfromotherpagesusingtheNewAdHoc Searchbuttonwillnotallowyoutoutilizethereportingfeatures

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CreatingReports

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• Let’ssayyouwanttoviewALL DNAandPBMCsamplesthatwerecollectedfortheIRBprotocol“Test123”betweenthedatesof4/1/2015-9/21/2015andyouwantyourreporttoincludethefollowingelements:firstname,lastname,MRN,externalpatientID,IRBprotocol,samplenumber,sampletype,anddatereceived

• First,setupyourAdhoc Queryasthoughyouweredoingasimplesearch

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CreatingReports

Page 23: LabVantage-Reports External V2 - University of Chicago · 2017-08-01 · IRB protocol “Test123” between the dates of 4/1/2015 -9/21/2015 • Select New AdHocQuery and select the

• Now,addtheelementsthatyouwanttoappearinthereportbyclickingontheViewColumnsicon

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CreatingReports

Page 24: LabVantage-Reports External V2 - University of Chicago · 2017-08-01 · IRB protocol “Test123” between the dates of 4/1/2015 -9/21/2015 • Select New AdHocQuery and select the

• NowaddtheelementthatyouwouldlikethereportsortedbyusingtheAddtoSortByColumnicon

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CreatingReports

Page 25: LabVantage-Reports External V2 - University of Chicago · 2017-08-01 · IRB protocol “Test123” between the dates of 4/1/2015 -9/21/2015 • Select New AdHocQuery and select the

• Now,clickeitherSearchNow(andthenExporttoExcelorExporttoPDF)orSearchandExportAlltoviewyourreport

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CreatingReports

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ForAdditionalHelp…

• PleaseseetheHTRCwebsiteformoreinformationandtofindadditionaltrainingresources:https://htrc.uchicago.edu

• OremailtheLabVantage administratorsat:[email protected]

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LabVantage - University of Chicago · IRB protocol “Test123” between the dates of 4/1/2015 -9/21/2015 • Select New AdHoc Query and select the search criteria from the left side

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LABORATORY KNOWLEDGE. DELIVERED.™ · PDF fileWhen a test is initiated by an inspection lot in SAP QM, the corresponding sample data will be created automatically in LABVANTAGE. In

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