biosense pla,orm data flow - amazon web services...biosense pla,orm data flow part 2 data ingeson...
TRANSCRIPT
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BioSensePla,ormDataFlow
Part2
DataInges5onintoESSENCE
DivisionofHealthInforma5csandSurveillance
March24,2016
CenterforSurveillance,Epidemiology,andLaboratoryServicesDivisionofHealthInformaDcsandSurveillance
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Agenda
§ IntroducDons§ BioSensePlaGormUpdate§ Recap:DataFlowintotheBioSensePlaGormArchive
§ ESSENCEOverview§ DataFlowintoESSENCE§ ESSENCEConsideraDons§ NextSteps
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BioSensePla,ormUpdateMichaelColeQa,MPH,NSSPProgramManager
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BioSensePla,ormUpdate
1.PLANNINGü CollaboratetoidenDfycriDcal
acDviDes
ü Collaboratetodeveloprequirements(AdminTool,
MasterFacilityTable)
ü Setupstagingenvironment
ü SetupproducDonenvironment
2.DEVELOPMENT
ü CreatebaselineMasterFacility
Tables
ü Documentdataflowo Establishdatamart
o DevelopUserAdminTool
o Researchsinglesign-onsoluDon
o AdjustESSENCEseNngso Developsupportdocuments
3.TRANSITIONo TransiDon9sitespermonth,
beginningsummer2016
o SunsetBioSenseWeb
applicaDon
o DevelopFacilityAdminTool
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RECAP:DataFlowintotheBioSensePla,ormArchiveRoseanneEnglish,BS,AnalyDcDataMgmt.TeamLead
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BioSensePla,ormDataFlowWebinars
Part1.DataInges5onintotheBioSensePla,orm
Part2.DataInges5onintoESSENCE
Part3.Migra5ngLegacyBioSenseData
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BioSensePla,ormDataFlowDiagram
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BioSensePla,ormArchive
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BioSensePla,ormArchiveModifica5ons
FeedbackfromBioSensePla6ormstakeholdershelpedtheNSSPteammodifyandimproveupontheArchiverequirements.
§ Repea5ngdataelementswillusesemicolon(;)separator;the|separatorcancauseissueswithESSENCEanddataprocessing
§ NEWComboFields(X_Combo)concatenatecodeswiththeirrespecDvedescripDonsassentinamessage
Diagnosis_Code
Diagnosis_Description Diagnosis_Combo
488.8;464 Influenza due to novel influenza A;Acute laryngitis and tracheitis
488.8 Influenza due to novel influenza A;464 Acute laryngitis and tracheitis
488;487 ;Influenza 488 ;487 Influenza
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BioSensePla,ormArchiveModifica5ons(conDnued)
§ CalculatedChiefComplaint(C_Chief_Complaint)—nowhierarchicallydefinedasthefirstnon-nullvaluefrom…o Chief_Complaint_Text (from TX or CWE data type)
o Admit_Reason_Description
§ CalculatedPa5entAgeo C_Patient_Age (Available in months if age < 2 years when
calculated from birth date and visit date)
o C_Patient_Age_Years (Normalized to an integer value for all age values and rounded down)
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BioSensePla,ormArchiveModifica5ons(conDnued)
§ CalculatedVisitDate—nowhierarchicallydefinedbyselecDngthefirstnon-nullvaluefrom…o Admit Date/Time (PV1-44)
o Earliest date among Discharge Date/Time (PV1.45.1), Procedure Date/Time (PR1.5.1), Patient Death Date/Time (PID.29.1), Recorded Date/Time of Message (EVN.2.1), or Date/Time of Message (MSH.7.1)
§ RemovedC_Valid_Visit_Dateelement
o If visit date cannot be calculated (is null) or is set in the future (compared to time of processing), that message will be stored in the Archive Exceptions table
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BioSensePla,ormArchiveModifica5ons(conDnued)
§ CalculatedPa5entClass—nolongerrestrictedtovaluesE,I,andO;settofirstnon-nullvalueamong:
o Patient_Class_Code—reported patient class from message
o C_FacType_Patient_Class—patient class inferred from facility type reported in the message
o C_MFT_Patient_Class—patient class associated with the primary facility from the MFT for the facility ID reported in the message
§ RevisedFacilityTypemappingtoPa5entClasso Proposal to map Urgent Care facilities to patient class
code of O (rather than previously proposed mapping to E)
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BioSensePla,ormArchiveModifica5ons(conDnued)
§ UniqueIDsgeneratedforprocessing
Processing clarification: if a patient visits a facility twice on the same day, messages for both interactions will be associated with the same C_BioSense_ID
Initial Name NEW Name Processing (updated) C_Unique_ Visit_ID
C_BioSense_ID
C_Visit_Date + C_Facility_ID (includes Site_ID) + C_Unique_Patient_ID
C_Processed_Visit_ID
C_Processed_ BioSense_ID
C_Visit_Date + C_Processed_Facility_ID (includes Site_ID and C_Patient_Class) + C_Unique_Patient_ID
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BioSensePla,ormArchiveModifica5ons(conDnued)
§ OBXsegmentprocessingo In X_Segment columns tied to coded elements from OBX
segments, the entire OBX segment will be stored (not just OBX-5 or OBX-6)
Received Chief Complaint as
Chief_ Complaint_Code
Chief_Complaint_Text
Chief_Complaint_ Segment
Chief_Complaint_Type
TX NULL STOMACHACHETHATHASLASTED2DAYS;NAUSEAANDVOMITING;MAYBEAFEVER
OBX|3|TX|8661-1^Chiefcomplaint^LN||STOMACHACHETHATHASLASTED2DAYS;NAUSEAANDVOMITING;MAYBEAFEVER
TX
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BioSensePla,ormArchiveModifica5ons(conDnued)
§ Addi5onofstringfieldsthatcapturedate/numerictypeinforma5onasastringtoenhanceprocessingo Message info is read into a string type field (Str_XXX) o String is then converted to datetime or numeric value o If string contains info not valid for that data type, the element is
null
Str_Birth_Date_Time Birth_Date_Time 19860501 1986-01-01 00:00:00:000 Yesterday . May 1 . May 1. 1986 1986-01-01 00:00:00:000
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BioSensePla,ormDataFlowWebinars
Part1.DataInges5onintotheBioSensePla,orm
Part2.DataInges5onintoESSENCE
Part3.Migra5ngLegacyBioSenseData
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ESSENCEOverviewMichaelColeQa,MPH,NSSPProgramManager
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ESSENCEFeatures
§ Adhocqueries§ Dashboards§ Interac5vemaps§ Interac5ve5meseriesgraphs§ Overview5meseriesgraphs
stra5fiedbykeyvariables§ Timeofarrivalanalysesfor
clusters§ Tableandcrosstabbuilder§ Interac5ve“pop-up”bar
charts
§ Self-definedalertswithadjustablesta5s5cs(“myalerts”)
§ Abilitytosharequeries§ Abilitytosharedashboards§ Abilitytosharesta5cor
dynamicbookmarks§ Recordsofinterestqueries§ Eventcommunica5onsystem§ Dynamicreporttemplates
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ESSENCEPilotFeedback
“…a lot of functionality and customizability.”
“…highly versatile . . . I can do so many things relevant to workflows I want to adopt when doing investigations.”
“The combined chief complaint and discharge diagnosis field allows querying on both fields simultaneously.”
“I like the options for streamlining my workflow—myESSENCE, myAlerts, and Report Manager.”
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DataFlowintoESSENCERoseanneEnglish,BS,AnalyDcDataMgmt.TeamLead
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DataFlowintoESSENCE
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SendingDatatoESSENCE
MessagesinArchiveProcessedTablewillbepushedtoESSENCEo For mapping documentation, see protected folder “NSSP Doc
Review” on ISDS Forum o Archive Processed and ESSENCE column names are generally the
same, with the exception of key fields for ESSENCE processing Guidingprinciplesforselec5ngdatatosendtoESSENCE
o Core elements in PHIN Guide for Syndromic Surveillance o Elements of analytic importance o Elements required to support ESSENCE processing o Timestamp information
Archive Processed Column ESSENCE Column
C_Facility_ID Hospital
C_Chief_Complaint ChiefcomplaintOrig
Diagnosis_Code DischargeDiagnosis
Discharge_Disposition_Code DischargeDisposition
Where possible, column names in the Archive and
in ESSENCE are the same
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DataFlowwithinESSENCE
Ingestion ER_Import_Staging
ER_Base
Detection (aberration detection
algorithms)
Web (e.g.,
Cache ER Base)
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ESSENCEInges5onProcessing–StagingTabletoBaseTable
§ ESSENCEapplica5onprocessesdatato…o Collapse messages into a single “visit” (using same algorithm to
identify a visit as the Archive column C_BioSense_ID) o Associate visits with specified syndromes and sub-syndromes
via Chief Complaint binning o Support Web-based queries
§ Foreachvisit,ESSENCEpopulateseachcolumnwithinfopresentinlastmessageprocessedforthatvisito ESSENCE enhancement: History fields (four elements now
have companion history fields that store info across all messages that constitute a single visit)
o Per community feedback, additional history fields may be added
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ESSENCEInges5onProcessing–StagingTabletoBaseTable(conDnued)
MessageDateTime C_Visit_Date_ Time
C_Unique_Patient_ID
Hospital (C_Facility_ID)
Sex Age
20160301 08:30:00:000
20160229 02:30:00:000
A12B3 001FACILITYID F .
20160301 08:40:00:000
20160229 02:30:00:000
A12B3 001FACILITYID . 40
20160301 09:30:00:000
20160229 01:30:00:000
123456 001FACILITYID M 22
ESSENCEID MessageDateTime
C_Visit_Date_ Time
C_Unique_Patient_ID
Hospital (C_Facility_ID)
Sex Age
20160229001FACILITYIDA12B3
20160301 08:40:00:000
20160229 02:30:00:000
A12B3 001FACILITYID . 40
20160229001FACILITYID123456
20160301 09:30:00:000
20160229 01:30:00:000
123456 001FACILITYID M 22
ER_Import_Staging (ESSENCE Staging Table)
ER_Base (ESSENCE Base Table)
Collapse to “Patient Event”
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HistoryField:Pa5entClass
§ TwoPa5entClassvariableswithcompanionhistoryfieldso PatientClass—maps to the patient class reported in the message
(Patient_Class_Code – PV1-2 – in the Archive) o C_Patient_Class—calculated patient class from the Archive
§ Lastreportedvaluefrommessage
§ De-duplicated,alphabe5callistofallvaluesreportedthroughoutavisit
§ Orderedlistofallreportedvaluesthroughoutavisit§ Timestamptodocumentwhenfieldswerelastupdated
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Example:Pa5entClassHistoryField
How does it work? Check out “PatientClassHistoryExample_Tool” in protected NSSP Doc Review folder on ISDS Forum.
ER Base Table PatientClass
PatientClass_H1 PatientClass_H2
E E|I E|I|E
ER Import StagingTable Message Order PatientClass 1 E 2 I 3 E
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HistoryField:ChiefComplaint
§ Firstreported,non-nullvalueforChiefComplaint§ De-duplicated,orderedlistofallChiefComplaintvaluessentacrossmessagesforasinglevisit
§ Timestamptodocumentwhenfieldswerelastupdated
Chief Complaint binning will run against values from a column named ChiefComplaintParsed, which contains parsed information from ChiefComplaintOrig. C_Chief_Complaint from the Archive populates ChiefComplaintOrig.
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Example:ChiefComplaintHistoryField
ER Base Table ChiefComplaintOrig ChiefComplaint_H1 My Original Chief Complaint
My Original Chief Complaint | Brief Chief Complaint |
ER Import Staging Table Message Number ChiefComplaintOrig 1 My Original Chief Complaint 2 Brief Chief Complaint 3
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HistoryField:DischargeDisposi5on
§ Lastreported,non-nullvalueforDischargeDisposi5on§ De-duplicated,orderedlistofallDischargeDisposi5onvaluessentacrossmessagesforasinglevisit
§ Timestamptodocumentthelast5methefieldswereupdated
DischargeDisposition is populated from
Discharge_Disposition (PV1-36) in the Archive.
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Example:DischargeDisposi5onHistoryField
ER Base Table DischargeDisposition DischargeDisposition
_H1 My First Discharge Disposition
| My First Discharge Disposition
ER Import StagingTable Message Number DischargeDisposition 1 2 My First Discharge
Disposition
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HistoryField:DischargeDiagnosis
§ Lastreported,non-nullvalueforDischargeDiagnosis§ De-duplicated,orderedlistofallDischargeDiagnosisvaluessentacrossmessagesforasinglevisit
§ Timestamptodocumentthelast5methefieldswereupdated
DischargeDiagnosis is populated from Diagnosis_Code (DG1) in the Archive.
DischargeDiagnosis is also appended to
ChiefComplaintParsed to create an analysis variable “CCDD” within ESSENCE.
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HistoryField:DischargeDiagnosis
ER Base Table DischargeDiagnosis DischargeDiagnosis
_H1 999;123 123;987 | 999;123 |
ER Import Staging Table Message Number DischargeDiagnosis 1 123;987 2 999;123 3
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ESSENCEQueryTool
UnderstandingthedatathatisavailableandhowitisprocessedmayinfluencetheconstrucDonofqueriesandcustomizaDonstotheQueryTool
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Ini5alESSENCESeNngsShayneGallaway,PhD,MPH,HealthScienDst
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Introduc5ontoESSENCESeNngs
§ ESSENCEseNngsallowuserconfigura5ons:o Customizable query capabilities o Syndrome-detection algorithms o Regional syndromes viewable by region, hospital, spatial,
and date/time o And many more!
§ Ini5alconsidera5onsforBioSensePla,orm:o Define the minimum data set viewable at national/state
levels (“National View”) o Define available data sources o Determine alert settings and related features
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Na5onalView
§ TheNa5onalViewwillbeaminimumdatasetaccessibletoallusersoftheBioSensePla,orm’sESSENCEapplica5on
§ WhatshouldbeincludedintheNa5onalView?
*PreviouslydiscussedwithBioSenseGovernanceGroup(Summer2015)
Some agreement* achieved To be discussed • Encounter date • Patient age, in 5-year age
groups • Patient gender • HHS Regions (10) • Syndrome • Sub-syndrome • Disposition
• Patient class • Time of arrival • Others?
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Na5onalView:ChiefComplaintandDiagnosisCode
§ Importanceo Chief Complaint and Diagnosis Code are used to develop
regional and national syndromic definitions
§ Challengeo Both fields may contribute to identifying information (alone or
in combination with other data)
§ Proposedsolu5on:o Segregate Chief Complaint and Diagnosis Code to enable
querying details o Results would not return other viewable details o Users can create and modify queries to capture syndromic
definitions of interest
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ESSENCEDataSources
§ Out-of-the-boxdatasourcesmayneedmodifica5onorclarifica5ontosupportBioSensePla,ormneedso ER Data by Patient Location (All, HHS Region, State and HHS
Region) o ER Data by Patient Location and Visit o ER Data by Hospital Location (All, Hosp HHS Region, Hosp
State and Hosp HHS Region) o ER Data by Hospital and Visit
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ESSENCEAlertSeNngs
§ Determinedatasourceforalertso Emergency Department? o Inpatient? o Urgent Care?
§ Knowwhatisandisnotincludedindatasource§ Iden5fyrelatedeventno5fica5ons§ DeterminestandardproceduresfortheReportsManager
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ESSENCEAlertSeNngs(conDnued)
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ESSENCESeNngs–Addi5onalTopics
§ Iden5fica5onofqueriablefields§ Queryoverviewparameters§ Viewabledetailsforselectedrecords§ Others
Wanttohelp?Usersofallexperiencelevelscan
contributetoESSENCEse_ngsandtooldevelopment
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Formoreinforma5onpleasecontactCentersforDiseaseControlandPreven5on1600Cli`onRoadNE,Atlanta,GA30329-4027Telephone:1-800-CDC-INFO(232-4636)/TTY:1-888-232-6348Visit:hQp://www.cdc.gov|ContactCDCat:1-800-CDC-INFOorhQp://www.cdc.gov/infoThefindingsandconclusionsinthisreportarethoseoftheauthorsanddonotnecessarilyrepresenttheofficialposiDonoftheCentersforDiseaseControlandPrevenDon.
CenterforSurveillance,Epidemiology,andLaboratoryServicesDivisionofHealthInformaDcsandSurveillance
MichaelA.ColeQa,MPHManager,NaDonalSyndromicSurveillanceProgramCDC/CSELS/[email protected]
Ques5ons?Weappreciateyourinput.