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

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Presentation on theme: "PCORI/GPC Standard Data Model Jim Campbell, Dan Connolly, GPC Data standardization team."— Presentation transcript:

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

2 GPC Data Standardization Workplan Agreed 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 dimension 2)Clinical Observables including biometrics; Clinical LOINC 3)Procedures; CPT and HCPCS 4)Laboratory Observables; Lab LOINC 5)Medications; RxNORM and NDF-RT 6)Diagnoses SNOMED CT

3 GPC Data Standardization Workplan Agreed 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

4 GPC Data Standardization Workplan Agreed 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)

5 GPC Data Standardization Workplan Publication 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’ 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) Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD …optional data (Data history) Visit_dimension PK 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_dimension PK Modifier_Path Modifier_CD Name_char (Data history)

7 PCORnet Common Data Model v1.0

8 GPC V1 Patient dimension Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD …optional data (Data history) Observation_fact 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 Concept_dimension Demographics\ \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:21838-8

9 GPC V1 Provider(observer) dimension Provider_dimension PK Provider_ID PK Observer_Path Name_char Provider_dimension PK Provider_ID PK Observer_Path Name_char (Data history) Observation_fact Observer_CD(NPI) LOINC:45952-9

10 GPC V1 Provider(observer) dimension Provider_dimension PK Provider_ID PK Observer_Path Name_char Provider_dimension PK Provider_ID PK 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_fact Observer_CD(NPI) LOINC:45952-9

11 GPC V1 Visit dimension Visit_dimension PK Encounter_num Patient_num Start_datetime End_datetime Active_status_CD Visit_dimension PK Encounter_num Patient_num Start_datetime End_datetime Active_status_CD …optional data (Data history) Observation_fact Inout_CD Facility_location(Zip3) Facility_CD(NPI) Discharge_disposition Discharge_status DRG DRG_type Admission_source Encounter_type_CD Service_type_CD Attending/billing_provider_CD Concept_dimension Encounters\ \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:52526-1

12 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)

13 GPC V1 Diagnoses 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 Observer_dimension PK Observer_Path Observer_CD (NPI) Name_char Concept_dimension1 PK Concept_Path Concept_CD (SNCT Clin Finding; Event;Situation) FullySpecifiedName_char Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Visit_dimension PK Encounter_num Start_datetime End_datetime Active_status_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 Modifier_dimension PK Dx_type_path DiagnosisType_CD Name_CHAR Modifiers Diagnosis 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

14 GPC V1 Clinical Measurements (Observable) 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 Concept_dimension PK Concept_Path Concept_CD(LOINC 2.38+) Name_char Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Visit_dimension PK Encounter_num Start_datetime End_datetime Active_status_CD Modifier_dimension PK Coded_result_Path Results_CD (SNCT) Name_char (Data history) Concept_dimension Observables\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

15 GPC V1 Procedures 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(HCPCS) Name_char Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Visit_dimension PK Encounter_num Start_datetime End_datetime Active_status_CD Modifier_dimension PK Proc_type_Path Procedure type_CD Name_CHAR (Data history) Concept_dimension PK Concept_Path Concept_CD(CPT) Name_char Modifiers Procedure Type \Billed \Surgical history

16 GPC V1 Enrollment 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 Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Modifier_dimension PK Proc_type_Path Procedure type_CD Name_CHAR (Data history) Enrollment Type \Insurance \Cohort membership

17 Lab Results (not batteries) 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 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 Modifier_dimension PK Coded_result_Path Results_CD (SNCT) Name_char (Data history)

18 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)| –…..

19 Lab Complex Results(micro & batteries) 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 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_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 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 Obs_Concept1 PK Concept_Path Concept_CD(SNCT Obs;LOINC) FullySpecifiedName_char Obs_ConceptN PK Concept_Path Concept_CD(SNCT Obs; LOINC) FullySpecifiedName_char

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

21 Allergy List 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 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 Allergenmodifier_dimension PK Modifier_Path Concept_CD(SNOMED CT) FullySpecifiedName_char Reactionmodifier_dimension PK Modifier_Path Concept_CD(SNOMED CT) FullySpecifiedName_char Sevmodifier_dimension 255604002|mild| 6736007|moderate| 24484000|severe| 399166001|fatal|

22 Medications administered 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 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 Routemodifier_dimension PK Concept_Path Concept_CD(<<406455002 <<410942007) FullySpecifiedName_char Dosemodifier_dimension PK Concept_Path Concept_CD(<<404684003) FullySpecifiedName_char modifier_dimension Administered Dispensed

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