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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 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. 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)

  9. 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 Location_CD(NPI) EncounterType_CD ServiceType_CD(CPT) Discharge_disposition Discharge_status DRG DRG_type Admission_source

  10. Concept dimension Concept_dimension PK Concept_Path Concept_CD Name_char (Data history) 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;

  11. Provider(observer) dimension Provider_dimension PK Provider_ID PK Observer_Path Name_char (Data history) Provider_dimension PK Provider_ID PK Observer_Path Name_char • Observer_CD(NPI) Role_CD(?)

  12. 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 DiagnosisType_CD 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

  13. 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 ModifiersDiagnosis Type Finding informer \116154003 Patient \303118004 Healthcare prv \... Subject relationship context \410604004 Subject of record \72705000 Mother 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(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. 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)

  15. 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)| • …..

  16. 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

  17. 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 Allergen_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 AllergyReaction_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 Sevmodifier_dimension 255604002|mild| 6736007|moderate| 24484000|severe| 399166001|fatal| Observer_dimension PK Observer_Path Observer_CD Name_char Role_CD Allergen_dimension PK Concept_Path Concept_CD(<<406455002 <<410942007) FullySpecifiedName_char Reaction_dimension PK Concept_Path Concept_CD(<<404684003) FullySpecifiedName_char AllergyList_dimension PK Concept_Path Concept_CD(<<418038007) FullySpecifiedName_char

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