PCORI/GPC Standard Data Model

Jim Campbell, Dan Connolly,

GPC Data standardization team

GPC Data Standardization WorkplanAgreed Hackathon 20140224

•I2b2 is our data repository tool; Star schema is the reference information model

•Domain 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 available

•Prioritized plan:1) Diagnoses; ICD-9-CM dimension2) Clinical Observables including biometrics; Clinical LOINC3) Procedures; CPT and HCPCS4) Laboratory Observables; Lab LOINC5) Medications; RxNORM and NDF-RT6) Diagnoses SNOMED CT

GPC Data Standardization WorkplanAgreed Hackathon 20140224

•EHR data extract (ETL) development will start with KU/Heron scripts and enhance them to align with model development and to include reference standards

•Model 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 reporting

•Data quality queries will be developed for site technical teams to assess their compliance with PCORI CDM

GPC Data Standardization WorkplanAgreed Hackathon 20140224

•Sites will either:–create identical ETL functionality in their own load scripts to standardize data model OR

–Those 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 20140330

•Data attributes required by the PCORI common data model will be supported in GPC

•Class definitions required by PCORI will be supported as query extract from GPC data when they are judged to be too restrictive for GPC class definitions

i2b2 ‘Out-of-the-box’

Observation_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_dimension

PK Concept_Path Concept_CD Name_char (Data history)

Patient_dimensionPK Patient_num Birth_date Death_date Vital_status_CD…optional 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 1.7.1

Modifier_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_CD…optional data (Data history)

Observation_factBirth_dateBirth_timeDeath_dateVital_status_CDSex_CD(HL7/OMBAge in years_numLanguage_CD(OMB)Race_CD(OMB)Marital_status_CD(OMB)Ethnicity_CD(OMB

Concept_dimensionDemographics\ \Vital_status LOINC:31210-8 \Birth_date LOINC:21112-8 \Birth_time LOINC:57715-5 \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:42784-9 \Religion LOINC:45823-2 \State residence LOINC:46499-0

GPC V1 Provider(observer) dimension

Provider_dimensionPK Provider_IDPK Observer_Path Name_char

Provider_dimensionPK Provider_IDPK Observer_Path Name_char (Data history)

Observation_factObserver_CD(NPI)LOINC:45952-9

GPC V1 Provider(observer) dimension

Provider_dimensionPK Provider_IDPK Observer_Path Name_char

Provider_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:45952-9

GPC 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_CD…optional data (Data history)

Observation_factInout_CDFacility_location(Zip3)Facility_CD(NPI)Discharge_dispositionDischarge_statusDRGDRG_typeAdmission_sourceEncounter_type_CDService_type_CDAttending/billing_provider_CD

Concept_dimensionEncounters\ \Inout_CD \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 \Encounter type_CD \Service type_CD(CPT) \Attending provider_num

GPC V1 Concept dimension•Demographics: LOINC, SNOMED CT observables

•Diagnoses: (Encounter dx; problem list; order dx; Nursing dx)SNOMED CT Clinical findings, events and situations / ICD-*-CM

•Observables: Lab tests: (laboratory, pathology) LOINC

•Observables: Clinical measurements (demographics; symptoms; physical findings): harmonized SNOMED CT Observables and LOINC

•Observables: Radiology tests: (Radiology tests and measurements): harmonized SNOMED CT Observables and LOINC

•Procedures: CPT / HCPCS / ICD* / SNOMED CT Procedures

•Substance administration: (Administered drugs, immunizations; immunologics ) NDFRT / RxNORM; CVX; MVX

•Orders\Meds\Procedures: (medication orders; prescriptions; testing) NDFRT/RXNORM;

Concept_dimensionPK Concept_Path Concept_CD Name_char (Data history)

GPC V1 Diagnoses

Diagnosis_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_Blob Observer_dimension

PK Observer_Path Observer_CD (NPI) Name_char

Concept_dimension1PK Concept_Path Concept_CD (SNCT Clin Finding; Event;Situation) FullySpecifiedName_char

Patient_dimensionPK Patient_num Birth_date Death_date Vital_status_CD

Visit_dimensionPK Encounter_num Start_datetime End_datetime Active_status_CD

Concept_dimension2PK Concept_Path Concept_CD (ICD-9-CM) FullySpecifiedName_char

Concept_dimension3PK Concept_Path Concept_CD (ICD-10-CM) FullySpecifiedName_char

Modifier_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_Blob

Observer_dimensionPK Observer_Path Observer_CD Name_char

Concept_dimensionPK Concept_Path Concept_CD(LOINC 2.38+) Name_char

Patient_dimensionPK Patient_num Birth_date Death_date Vital_status_CD

Visit_dimensionPK Encounter_num Start_datetime End_datetime Active_status_CD

Modifier_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:8462-4

GPC V1 Procedures

Observation_factPK Patient_numPK Encounter_numPK Concept_CDPK Observer_CDPK Start_datePK Modifier_CDPK Instance_num End_date Tval_Char Nval_Num ValueFlag_CD Observation_Blob

Observer_dimensionPK Observer_Path Observer_CD Name_char Role_CD

Concept_dimensionPK Concept_Path Concept_CD(HCPCS) Name_char

Patient_dimensionPK Patient_num Birth_date Death_date Vital_status_CD

Visit_dimensionPK Encounter_num Start_datetime End_datetime Active_status_CD

Modifier_dimensionPK Proc_type_Path Procedure type_CD Name_CHAR (Data history)

Concept_dimensionPK Concept_Path Concept_CD(CPT) Name_char Modifiers Procedure Type

\Billed \Surgical history

GPC V1 Enrollment

Observation_factPK Patient_numPK Encounter_numPK Concept_CDPK Observer_CDPK Start_datePK Modifier_CDPK Instance_num End_date Tval_Char Nval_Num ValueFlag_CD Observation_Blob

Observer_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_CD

Modifier_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_Blob

Observer_dimensionPK Observer_Path Observer_CD Name_char Role_CD

Concept_dimensionPK Concept_Path Concept_CD(LOINC 2.38+) Name_char

Patient_dimensionPK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD

Visit_dimensionPK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD EncounterType_CD ServiceType_CD

Modifier_dimensionPK Coded_result_Path Results_CD (SNCT) Name_char (Data history)