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

•Tentative plan:–Diagnoses; ICD-9-CM dimension–Clinical Observables including biometrics; Clinical LOINC–Laboratory Observables; LOINC–Medications; RxNORM and NDF-RT

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; these will be our 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

GPC Data Standardization WorkplanAgreed Hackathon 20140224

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

•Sites 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

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 Sex_CD Age_in_years_num Language_CD Race_CD Marital_status_CD …optional data (Data history)

Visit_dimensionPK Encounter_num Patient_num Start_datetime End_datetime Active_status_CD Inout_CD Location_CD Visit_blob …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

Patient dimension

Patient_dimensionPK Patient_num Birth_date Death_date Vital_status_CD Sex_CD(HL7/OMB) Age_in_years_num Language_CD(OMB) Race_CD(OMB) Marital_status_CD(OMB) Ethnicity_CD(OMB)

Patient_dimensionPK Patient_num Birth_date Death_date Vital_status_CD Sex_CD Age_in_years_num Language_CD Race_CD Marital_status_CD …optional data (Data history)

Visit dimensionVisit_dimensionPK Encounter_num Patient_num Start_datetime End_datetime Active_status_CD Inout_CD Facility_location Location_CD(NPI) EncounterType_CD ServiceType_CD(CPT) Discharge_disposition Discharge_status DRG DRG_type Admission_source

Visit_dimensionPK Encounter_num Patient_num Start_datetime End_datetime Active_status_CD Inout_CD Location_CD Visit_blob …optional data (Data history)

Concept dimension

•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: SNOMED CT Procedures / CPT / HCPCS

•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)

Provider(observer) dimension

Provider_dimensionPK Provider_IDPK Observer_Path Name_char Observer_CD (NPI) Role_CD(?)

Provider_dimensionPK Provider_IDPK Observer_Path Name_char (Data history)

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 Role_CD

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

Concept_dimension2PK Concept_Path Concept_CD (ICD-9-CM) FullySpecifiedName_char

Concept_dimension3PK Concept_Path Concept_CD (ICD-10-CM) FullySpecifiedName_char

Modifier_dimension DiagnosisType_CD

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

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 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)

Weight observable BMI 39156-5; 60621009 BMI% (age and gender) 59576-9 Weight (measured) 3141-9;; 27113001 Height 8302-2; 50373000

Concept_dimensionPK Concept_Path Concept_CD(SNOMED observable) Name_char

Modifiers Diagnosis TypeFinding informer \116154003 Patient \303118004 Healthcare prv \... Subject relationship context \410604004 Subject of record \72705000 Mother

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)

Culture report coding

• Urine 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/ml– Susceptibility 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_CD

Observer_dimensionPK Observer_Path Observer_CD Name_char Role_CD

Battery_ConceptPK Concept_Path Concept_CD(SNCT Proc; LOINC) FullySpecifiedName_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_CDObservation_fact1

PK 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_CD

Observation_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_CD

Obs_Concept1PK Concept_Path Concept_CD(SNCT Obs;LOINC) FullySpecifiedName_char

Obs_ConceptNPK Concept_Path Concept_CD(SNCT Obs; LOINC) FullySpecifiedName_char

Allergy List

AllergyList_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_Blob

Observer_dimensionPK Observer_Path Observer_CD Name_char Role_CD

AllergyList_dimensionPK Concept_Path Concept_CD(<<418038007) FullySpecifiedName_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

Allergen_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_Blob

AllergyReaction_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_Blob

Allergen_dimensionPK Concept_Path Concept_CD(<<406455002 <<410942007) FullySpecifiedName_char

Reaction_dimensionPK Concept_Path Concept_CD(<<404684003) FullySpecifiedName_char

Sevmodifier_dimension 255604002|mild| 6736007|moderate| 24484000|severe| 399166001|fatal|