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PCORI/G PC Standard Data Model

PCORI/G PC Standard Data Model. Jim Campbell, Dan Connolly, GPC Data standardization team. GPC Data Standardization Workplan Agreed Hackathon 20140224. I2b2 is our data repository tool; Star schema is the reference information model

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PCORI/G PC Standard Data Model

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  1. PCORI/GPC Standard Data Model Jim Campbell, Dan Connolly, GPC Data standardization team

  2. 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

  3. 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

  4. 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

  5. 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

  6. i2b2 ‘Out-of-the-box’ Visit_dimension PK Encounter_num Patient_num Start_datetime End_datetime Active_status_CD Inout_CD Location_CD Visit_blob …optional data (Data history) Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Sex_CD Age_in_years_num Language_CD Race_CD Ethnicity_CD Marital_status_CD • …optional data • (Data history) Observation_fact Patient_num PK Encounter_num PK Concept_CD PK Provider_ID PK 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_dimension PK Provider_ID PK Observer_Path Name_char (Data history) Concept_dimension PK Concept_Path Concept_CD Name_char (Data history) Modifier_dimension PK Modifier_Path Modifier_CD Name_char (Data history) I2b2 Design Document; Data Repository (CRC) Cell; Partners Healthcare System; document version 1.7.1

  7. PCORnet Common Data Model v1.0

  8. GPC V1 Patient dimension Patient_dimension PK 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) Patient_dimension PK 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) Observation_fact Birth_date Death_date Vitals_status_CD Sex_CD Age in years_num Language_CD Race_CD Marital_status_CD Ethnicity_CD Concept_dimension Demographics\ \Vitals_status \Sex \Age \Language \Residence \Race \Marital_status \Ethnicity

  9. GPC V1 Provider(observer) dimension Provider_dimension PK Provider_ID PK Observer_Path Name_char (Data history) Observer_Path (DRAFT) =<<SNCT25676002|Person| <<|Guardian| <<|Partner in relationship| <<Person in the family| <<Person in healthcare| What Provider_ID for a patient? Provider_dimension PK Provider_ID PK Observer_Path Name_char • Observer_CD(NPI) (Observer_gender_CD)

  10. GPC V1 Visit dimension Visit_dimension PK Encounter_num Patient_num Start_datetime End_datetime Active_status_CD Inout_CD Location_CD Visit_blob …optional data (Data history) Visit_dimension PK Encounter_num Patient_num Start_datetime End_datetime Active_status_CD Inout_CD Facility_location EncounterType_CD ServiceType_CD(CPT) FK Provider_ID Observation_fact Facility_CD(NPI) Discharge_disposition Discharge_status DRG DRG_type Admission_source PCORI CDM Issues Facility location 3 digit zip Add provider to visit dimension; include DRG etc as Observation Facts or as Encounter atts? 46579-9 Discharge disposition 52523-8 Discharge status 38999-9 Discharge DRG (modifier for DRG type?) 57830-2 Admission request?add

  11. 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_dimension PK Concept_Path Concept_CD Name_char (Data history)

  12. GPC V1 Diagnoses Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Visit_dimension PK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD EncounterType_CD ServiceType_CD ModifiersDiagnosis Type Billing dx \Admission \Discharge principal \Discharge present on adm \Discharge secondary Encounter dx \admission \discharge dx \discharge dx primary \discharge dx secondary Medical history dx Order dx \med order \procedure order Problem list dx \active \deleted \resolved Prof billing dx \primary \secondary Diagnosis_fact1 PK Patient_num PK Encounter_num PK Concept_CD PK Observer_CD PK Start_date PK Modifier_CD PK Instance_num End_date Valtype_CD Tval_Char Nval_Num ValueFlag_CD Observation_Blob Modifier_dimension PK Dx_type_path DiagnosisType_CD Name_CHAR Concept_dimension1 PK Concept_Path Concept_CD (SNCT Clin Finding; Event;Situation) FullySpecifiedName_char Observer_dimension PK Observer_Path Observer_CD (NPI) Name_char Role_CD Concept_dimension2 PK Concept_Path Concept_CD (ICD-9-CM) FullySpecifiedName_char Concept_dimension3 PK Concept_Path Concept_CD (ICD-10-CM) FullySpecifiedName_char What distinction are we Drawing between encounters And billing diagnoses?

  13. GPC V1 Clinical Measurements(Observable) Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Visit_dimension PK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD EncounterType_CD ServiceType_CD Observation_fact PK Patient_num PK Encounter_num PK Concept_CD PKObserver_CD PK Start_date PK Modifier_CD PK Instance_num End_date Tval_Char Nval_Num ValueFlag_CD Observation_Blob Observer_dimension PK Observer_Path Observer_CD Name_char Role_CD Observable Systolic BP 8480-6 Diastolic BP 8462-4 Body position 8361-8 Systolic BP sitting 8459-0 Diastolic BP sitting 8453-3 Concept_dimension PK Concept_Path Concept_CD(SNOMED observable) Name_char Concept_dimension PK Concept_Path Concept_CD(LOINC 2.38+) Name_char Modifier_dimension PK 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

  14. GPC V1 Procedures Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Visit_dimension PK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD EncounterType_CD ServiceType_CD Observation_fact PK Patient_num PK Encounter_num PK Concept_CD PK Observer_CD PK Start_date PK Modifier_CD PK Instance_num End_date Tval_Char Nval_Num ValueFlag_CD Observation_Blob Observer_dimension PK Observer_Path Observer_CD Name_char Role_CD Concept_dimension PK Concept_Path Concept_CD(CPT) Name_char Concept_dimension PK Concept_Path Concept_CD(HCPCS) Name_char Modifier_dimension PK Proc_type_Path Procedure type_CD Name_CHAR (Data history) ModifiersProcedure Type \Billed \Surgical history Concept_dimension PK Concept_Path Concept_CD(ICD-9-PCS) Name_char Concept_dimension PK Concept_Path Concept_CD(ICD-10-PCS) Name_char Concept_dimension PK Concept_Path Concept_CD(ISNOMED CT) Name_char

  15. GPC V1 Enrollment Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Observation_fact PK Patient_num PK Encounter_num PK Concept_CD PK Observer_CD PK Start_date PK Modifier_CD PK Instance_num End_date Tval_Char Nval_Num ValueFlag_CD Observation_Blob Observer_dimension PK Observer_Path Observer_CD Name_char Role_CD Modifier_dimension PK Proc_type_Path Procedure type_CD Name_CHAR (Data history) Enrollment Type \Insurance \Cohort membership

  16. Lab Results (not batteries) Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Visit_dimension PK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD EncounterType_CD ServiceType_CD Observation_fact PK Patient_num PK Encounter_num PK Concept_CD PKObserver_CD PK Start_date PK Modifier_CD PK Instance_num End_date Tval_Char Nval_Num ValueFlag_CD Observation_Blob Observer_dimension PK Observer_Path Observer_CD Name_char Role_CD Concept_dimension PK Concept_Path Concept_CD(LOINC 2.38+) Name_char Modifier_dimension PK Coded_result_Path Results_CD (SNCT) Name_char (Data history)

  17. 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)| • …..

  18. Lab Complex Results(micro & batteries) Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Visit_dimension PK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD EncounterType_CD ServiceType_CD Observation_factN PK Patient_num PK Encounter_num PK Concept_CD PK Observer_CD PK Start_date PK Modifier_CD PK Instance_numcom End_date Valtype_CD Tval_Char Nval_Num ValueFlag_CD Observation_Blob Valcode_CD Observation_fact1 PK Patient_num PK Encounter_num PK Concept_CD PK Observer_CD PK Start_date PK Modifier_CD PK Instance_numcom End_date Valtype_CD Tval_Char Nval_Num ValueFlag_CD Observation_Blob Valcode_CD Battery_fact PK Patient_num PK Encounter_num PK Concept_CD PK Observer_CD PK Start_date PK Modifier_CD PK Instance_numcom End_date Valtype_CD Tval_Char Nval_Num ValueFlag_CD Observation_Blob Valcode_CD Observer_dimension PK Observer_Path Observer_CD Name_char Role_CD Battery_Concept PK Concept_Path Concept_CD(SNCT Proc; LOINC) FullySpecifiedName_char Obs_Concept1 PK Concept_Path Concept_CD(SNCT Obs;LOINC) FullySpecifiedName_char Obs_ConceptN PK Concept_Path Concept_CD(SNCT Obs; LOINC) FullySpecifiedName_char

  19. Allergy record • Concept dimension: • Sensitivity type: Allergy, pseudoallergy, intolerance, contraindication • Modifier dimensions: • Allergen: Drug or immunologic, substance, food • Reaction • Criticality • Severity

  20. Allergy List Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Visit_dimension PK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD EncounterType_CD ServiceType_CD AllergyList_fact PK Patient_num PK Encounter_num PK Concept_CD PK Observer_CD PK Start_date PK Modifier_CD PK Instance_num End_date Valtype_CD Tval_Char Nval_Num ValueFlag_CD Observation_Blob Observer_dimension PK Observer_Path Observer_CD Name_char Role_CD AllergySensitivity_dimension PK Concept_Path Concept_CD(<<418038007) FullySpecifiedName_char Sevmodifier_dimension 255604002|mild| 6736007|moderate| 24484000|severe| 399166001|fatal| Reactionmodifier_dimension PK Modifier_Path Concept_CD(SNOMED CT) FullySpecifiedName_char Allergenmodifier_dimension PK Modifier_Path Concept_CD(SNOMED CT) FullySpecifiedName_char

  21. Medications administered Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Visit_dimension PK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD EncounterType_CD ServiceType_CD AllergyList_fact PK Patient_num PK Encounter_num PK Concept_CD PK Observer_CD PK Start_date PK Modifier_CD PK Instance_num End_date Valtype_CD Tval_Char Nval_Num ValueFlag_CD Observation_Blob Observer_dimension PK Observer_Path Observer_CD Name_char Role_CD AllergySensitivity_dimension PK Concept_Path Concept_CD(<<418038007) FullySpecifiedName_char modifier_dimension Administered Dispensed Dosemodifier_dimension PK Concept_Path Concept_CD(<<404684003) FullySpecifiedName_char Routemodifier_dimension PK Concept_Path Concept_CD(<<406455002 <<410942007) FullySpecifiedName_char

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