PCORI/GPC Standard Data Model

PCORI/GPC Standard Data ModelJim Campbell, Dan Connolly, GPC Data standardization teamGPC Data Standardization WorkplanAgreed Hackathon 20140224I2b2 is our data repository tool; Star schema is the reference information modelDomain ontologies, code sets and value sets will be discussed and agreed by GPC/DEV on staged plan prioritized for our research teams; we will follow ONC advice whenever availablePrioritized plan:Diagnoses; ICD-9-CM dimensionClinical Observables including biometrics; Clinical LOINCProcedures; CPT and HCPCSLaboratory Observables; Lab LOINCMedications; RxNORM and NDF-RTDiagnoses SNOMED CTGPC Data Standardization WorkplanAgreed Hackathon 20140224EHR data extract (ETL) development will start with KU/Heron scripts and enhance them to align with model development and to include reference standardsModel development will include population quantification and data quality metrics that will standardize reporting to GPC; test queries for i2b2 research data will be developed by the three research teams as their objectives become clear and supplied to GPC STD/DEV for quality assurance reportingData quality queries will be developed for site technical teams to assess their compliance with PCORI CDM

GPC Data Standardization WorkplanAgreed Hackathon 20140224Sites will either:create identical ETL functionality in their own load scripts to standardize data model ORThose not capable of supporting standard test query functionality by virtue of inability to meet standardization scheduling will map their i2b2 repositories to meet query functional requirements at a time agreed upon by GPC/DEV (7/1/2014 for CDM V1)GPC Data Standardization WorkplanPublication PCORI CDM 20140330Data attributes required by the PCORI common data model will be supported in GPCClass definitions required by PCORI will be supported as query extract from GPC data when they are judged to be too restrictive for GPC class definitionsi2b2 Out-of-the-boxObservation_fact Patient_numPK Encounter_numPK Concept_CDPK Provider_IDPK Start_date Modifier_CD Instance_num End_date Valtype_CD Tval_Char Nval_Num ValueFlag_CD Quantity_num Units_CD Location_CD Observation_Blob Confidence_num (Data history)Provider_dimensionPK Provider_IDPK Observer_Path Name_char (Data history)

Concept_dimensionPK Concept_Path Concept_CD Name_char (Data history)Patient_dimensionPK Patient_num Birth_date Death_date Vital_status_CDoptional data (Data history) Visit_dimensionPK Encounter_num Patient_num Start_datetime End_datetime Active_status_CD optional data (Data history)I2b2 Design Document; Data Repository (CRC) Cell; Partners Healthcare System; document version 1.7.1Modifier_dimensionPK Modifier_Path Modifier_CD Name_char (Data history)

PCORnet Common Data Model v1.0

GPC V1 Patient dimensionPatient_dimensionPK Patient_num Birth_date Death_date Vital_status_CD Patient_dimensionPK Patient_num Birth_date Death_date Vital_status_CDoptional data (Data history) Observation_factBirth_dateDeath_dateVital_status_CDSex_CD(HL7/OMBAge in years_numLanguage_CD(OMB)Race_CD(OMB)Marital_status_CD(OMB)Ethnicity_CD(OMBConcept_dimensionDemographics\ \Vital_status LOINC:31210-8 \Sex LOINC:21840-4 \Age LOINC:30525-0 \Language LOINC:54899-0 \Residence LOINC:46526-0 \Race LOINC:32624-9 \Marital_status LOINC:45404-1 \Ethnicity LOINC:21838-8GPC V1 Provider(observer) dimensionProvider_dimensionPK Provider_IDPK Observer_Path Name_charProvider_dimensionPK Provider_IDPK Observer_Path Name_char (Data history)

Observation_factObserver_CD(NPI)LOINC:45952-9GPC V1 Provider(observer) dimensionProvider_dimensionPK Provider_IDPK Observer_Path Name_charProvider_dimensionPK Provider_IDPK Observer_Path Name_char (Data history)

Observer_Path (DRAFT)

SNCT25676002|Person| 394619001|Guardian| 58626006|Legal guardian| 262043009|Partner in relationship| |Common-law husband| |Common-law wife| |Domestic partner| |Spouse| 303071001|Person in the family| |Adopted person| |Adopted child| |Relative| |Immediate family member| |Child| |Parent| |Sibling| |Person in healthcare environment| |Caregiver| |Patient| |Healthcare professional| |Medical practitioner| |Physician| |Surgeon| |Health visitors nurses and midwives| |Professional nurse| |Professional midwife|Observation_factObserver_CD(NPI)LOINC:45952-9GPC V1 Visit dimensionVisit_dimensionPK Encounter_num Patient_num Start_datetime End_datetime Active_status_CD Visit_dimensionPK Encounter_num Patient_num Start_datetime End_datetime Active_status_CDoptional data (Data history)Observation_factInout_CDFacility_location(Zip3)Facility_CD(NPI)Discharge_dispositionDischarge_statusDRGDRG_typeAdmission_sourceEncounter_type_CDService_type_CDAttending/billing_provider_CDConcept_dimensionEncounters\ \Inout_CD LOINC:59543-9 \Facility_location(zip) LOINC:52831-5 \Facility_CD(NPI) LOINC:44960-3 \Discharge_disposition LOINC:46579-9 \Discharge status LOINC:52523-8 \Discharge DRG LOINC: 38999-9 \Admission source LOINC:52536-0 \Encounter type_CD LOINC:57122-4 \Service type_CD(CPT) \Attending provider_num LOINC:52526-1GPC V1 Concept dimensionDemographics: LOINC, SNOMED CT observablesDiagnoses: (Encounter dx; problem list; order dx; Nursing dx)SNOMED CT Clinical findings, events and situations / ICD-*-CMObservables: Lab tests: (laboratory, pathology) LOINCObservables: Clinical measurements (demographics; symptoms; physical findings): harmonized SNOMED CT Observables and LOINCObservables: Radiology tests: (Radiology tests and measurements): harmonized SNOMED CT Observables and LOINCProcedures: CPT / HCPCS / ICD* / SNOMED CT Procedures Substance administration: (Administered drugs, immunizations; immunologics ) NDFRT / RxNORM; CVX; MVXOrders\Meds\Procedures: (medication orders; prescriptions; testing) NDFRT/RXNORM;

Concept_dimensionPK Concept_Path Concept_CD Name_char (Data history)GPC V1 DiagnosesDiagnosis_fact1PK Patient_numPK Encounter_numPK Concept_CDPK Observer_CDPK Start_datePK Modifier_CDPK Instance_num End_date Valtype_CD Tval_Char Nval_Num ValueFlag_CD Observation_BlobObserver_dimensionPK Observer_Path Observer_CD (NPI) Name_charConcept_dimension1PK Concept_Path Concept_CD (SNCT Clin Finding; Event;Situation) FullySpecifiedName_charPatient_dimensionPK Patient_num Birth_date Death_date Vital_status_CD Visit_dimensionPK Encounter_num Start_datetime End_datetime Active_status_CDConcept_dimension2PK Concept_Path Concept_CD (ICD-9-CM) FullySpecifiedName_charConcept_dimension3PK Concept_Path Concept_CD (ICD-10-CM) FullySpecifiedName_charModifier_dimensionPK Dx_type_path DiagnosisType_CD Name_CHAR

Modifiers Diagnosis TypeBilling dx \Admission \Discharge principal \Discharge present on adm \Discharge secondaryEncounter dx \admission \discharge dx \discharge dx primary \discharge dx secondaryMedical history dxOrder dx \med order \procedure orderProblem list dx \active \deleted \resolvedProf billing dx \primary \secondary

GPC V1 Clinical Measurements(Observable)Observation_factPK Patient_numPK Encounter_numPK Concept_CDPKObserver_CDPK Start_datePK Modifier_CDPK Instance_num End_date Tval_Char Nval_Num ValueFlag_CD Observation_BlobObserver_dimensionPK Observer_Path Observer_CD Name_char

Concept_dimensionPK Concept_Path Concept_CD(LOINC 2.38+) Name_charPatient_dimensionPK Patient_num Birth_date Death_date Vital_status_CDVisit_dimensionPK Encounter_num Start_datetime End_datetime Active_status_CDModifier_dimensionPK Coded_result_Path Results_CD (SNCT) Name_char (Data history)

Concept_dimensionObservables\Clinical\ \Height LOINC:8302-2 \Length LOINC:3137-7 \Weight LOINC:3141-9 \BMI LOINC:39156-5 \Systolic BP LOINC:8480-6 \Diastolic BP LOINC:8462-4GPC V1 ProceduresObservation_factPK Patient_numPK Encounter_numPK Concept_CDPK Observer_CDPK Start_datePK Modifier_CDPK Instance_num End_date Tval_Char Nval_Num ValueFlag_CD Observation_BlobObserver_dimensionPK Observer_Path Observer_CD Name_char Role_CD

Concept_dimensionPK Concept_Path Concept_CD(HCPCS) Name_charPatient_dimensionPK Patient_num Birth_date Death_date Vital_status_CDVisit_dimensionPK Encounter_num Start_datetime End_datetime Active_status_CDModifier_dimensionPK Proc_type_Path Procedure type_CD Name_CHAR (Data history)

Concept_dimensionPK Concept_Path Concept_CD(CPT) Name_charModifiers Procedure Type \Billed \Surgical history

GPC V1 EnrollmentObservation_factPK Patient_numPK Encounter_numPK Concept_CDPK Observer_CDPK Start_datePK Modifier_CDPK Instance_num End_date Tval_Char Nval_Num ValueFlag_CD Observation_BlobObserver_dimensionPK Observer_Path Observer_CD Name_char Role_CD

Patient_dimensionPK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CDModifier_dimensionPK Proc_type_Path Procedure type_CD Name_CHAR (Data history)

Enrollment Type \Insurance \Cohort membership

Lab Results (not batteries)Observation_factPK Patient_numPK Encounter_numPK Concept_CDPKObserver_CDPK Start_datePK Modifier_CDPK Instance_num End_date Tval_Char Nval_Num ValueFlag_CD Observation_BlobObserver_dimensionPK Observer_Path Observer_CD Name_char Role_CD

Concept_dimensionPK Concept_Path Concept_CD(LOINC 2.38+) Name_charPatient_dimensionPK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CDVisit_dimensionPK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD EncounterType_CD ServiceType_CDModifier_dimensionPK Coded_result_Path Results_CD (SNCT) Name_char (Data history)

Culture report codingUrine culture 117010004|Urine culture (procedure)|Specimen (LNC31208-2): SNCT258574006|mid-stream urine sample(specimen)|Organism (LNC41852-5): SNCT112283007|E coli(organism)|Colony count (LNC49223-1): 10^6 col/mlSusceptibility to ampicillin/agar diffusion (LNC33-1): SNCT30714006|Resistant(qualifier)|Susceptibility to Bactrim/agar diffusion(LNC517-3): SNCT131196009|Susceptible(qualifier)|..

Lab Complex Results(micro & batteries)Battery_factPK Patient_numPK Encounter_numPK Concept_CDPK Observer_CDPK Start_datePK Modifier_CDPK Instance_numcom End_date Valtype_CD Tval_Char Nval_Num ValueFlag_CD Observation_Blob Valcode_CDObserver_dimensionPK Observer_Path Observer_CD Name_char Role_CD

Battery_ConceptPK Concept_Path Concept_CD(SNCT Proc; LOINC) FullySpecifiedName_charPatient_dimensionPK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CDVisit_dimensionPK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD EncounterType_CD ServiceType_CDObservation_fact1PK Patient_numPK Encounter_numPK Concept_CDPK Observer_CDPK Start_datePK Modifier_CDPK Instance_numcom End_date Valtype_CD Tval_Char Nval_Num ValueFlag_CD Observation_Blob Valcode_CDObservation_factNPK Patient_numPK Encounter_numPK Concept_CDPK Observer_CDPK Start_datePK Modifier_CDPK Instance_numcom End_date Valtype_CD Tval_Char Nval_Num ValueFlag_CD Observation_Blob Valcode_CDObs_Concept1PK Concept_Path Concept_CD(SNCT Obs;LOINC) FullySpecifiedName_charObs_ConceptNPK Concept_Path Concept_CD(SNCT Obs; LOINC) FullySpecifiedName_char

Allergy recordConcept dimension:Sensitivity type: Allergy, pseudoallergy, intolerance, contraindicationModifier dimensions:Allergen: Drug or immunologic, substance, foodReactionCriticalitySeverityAllergy ListAllergyList_factPK Patient_numPK Encounter_numPK Concept_CDPK Observer_CDPK Start_datePK Modifier_CDPK Instance_num End_date Valtype_CD Tval_Char Nval_Num ValueFlag_CD Observation_BlobObserver_dimensionPK Observer_Path Observer_CD Name_char Role_CD

AllergySensitivity_dimensionPK Concept_Path Concept_CD(