PCORIGPC Standard Data Model Jim Campbell Dan Connolly
PCORI/GPC Standard Data Model Jim Campbell, Dan Connolly, GPC Data standardization team
GPC Data Standardization Workplan Agreed Hackathon 20140224 • I 2 b 2 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; Rx. NORM and NDF-RT
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; 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 i 2 b 2 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 Workplan Agreed 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 i 2 b 2 repositories to meet query functional requirements at a time agreed upon by GPC/DEV
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
i 2 b 2 ‘Out-of-the-box’ Visit_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) Concept_dimension PK Concept_Path Concept_CD Name_char (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 Value. Flag_CD Quantity_num Units_CD Location_CD Observation_Blob Confidence_num (Data history) PK Encounter_num Patient_num Start_datetime End_datetime Active_status_CD Inout_CD Location_CD Visit_blob …optional data (Data history) Provider_dimension PK Provider_ID PK Observer_Path Name_char (Data history) Modifier_dimension PK Modifier_Path Modifier_CD Name_char (Data history) I 2 b 2 Design Document; Data Repository (CRC) Cell; Partners Healthcare System; document version 1. 7. 1
PCORnet Common Data Model v 1. 0
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(HL 7/OMB) Age_in_years_num Language_CD(OMB) Race_CD(OMB) Marital_status_CD(OMB) Ethnicity_CD(OMB)
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) Encounter. Type_CD Service. Type_CD(CPT) Discharge_disposition Discharge_status DRG_type Admission_source
Concept_dimension PK Concept_Path Concept_CD Name_char (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 / Rx. NORM; CVX; MVX • OrdersMedsProcedures: (medication orders; prescriptions; testing) NDFRT/RXNORM;
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(? )
Diagnoses Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Concept_dimension 1 PK Concept_Path Concept_CD (SNCT Clin Finding; Event; Situation) Fully. Specified. Name_char Concept_dimension 2 PK Concept_Path Concept_CD (ICD-9 -CM) Fully. Specified. Name_char Concept_dimension 3 PK Concept_Path Concept_CD (ICD-10 -CM) Fully. Specified. Name_char Visit_dimension Diagnosis_fact 1 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 Value. Flag_CD Observation_Blob PK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD Encounter. Type_CD Service. Type_CD Modifiers Diagnosis Type Billing dx Admission Discharge principal Discharge present on adm Discharge secondary Modifier_dimension Encounter dx Diagnosis. Type_CD admission discharge dx primary discharge dx secondary Observer_dimension Medical history dx PK Observer_Path Order dx Observer_CD (NPI) med order Name_char Role_CD procedure order Problem list dx active deleted resolved Prof billing dx primary secondary
Clinical Measurements (Observable) Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Concept_dimension PK Concept_Path Concept_CD(SNOMED observable) Name_char Concept_dimension Visit_dimension 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 Value. Flag_CD Observation_Blob PK Concept_Path Concept_CD(LOINC 2. 38+) Name_char Weight observable BMI% (age and gender) Weight (measured) Height 39156 -5; 60621009 59576 -9 3141 -9; ; 27113001 8302 -2; 50373000 PK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD Encounter. Type_CD Service. Type_CD Observer_dimension PK Observer_Path Observer_CD Name_char Role_CD Modifier_dimension PK Coded_result_Path Results_CD (SNCT) Name_char (Data history) Modifiers Diagnosis Type Finding informer 116154003 Patient 303118004 Healthcare prv . . . Subject relationship context 410604004 Subject of record 72705000 Mother
Lab Results (not batteries) Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Concept_dimension PK Concept_Path Concept_CD(LOINC 2. 38+) Name_char Visit_dimension 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 Value. Flag_CD Observation_Blob PK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD Encounter. Type_CD Service. Type_CD Observer_dimension PK Observer_Path Observer_CD Name_char Role_CD Modifier_dimension PK Coded_result_Path Results_CD (SNCT) Name_char (Data history)
Culture report coding • Urine culture 117010004|Urine culture (procedure)| – Specimen (LNC 31208 -2): SNCT 258574006|mid-stream urine sample(specimen)| – Organism (LNC 41852 -5): SNCT 112283007|E coli(organism)| – Colony count (LNC 49223 -1): 10^6 col/ml – Susceptibility to ampicillin/agar diffusion (LNC 33 -1): SNCT 30714006|Resistant(qualifier)| – Susceptibility to Bactrim/agar diffusion(LNC 517 -3): SNCT 131196009|Susceptible(qualifier)| – …. .
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 Battery_Concept Visit_dimension Battery_fact Observation_fact 1 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 Value. Flag_CD Observation_Blob Valcode_CD PK Concept_Path Concept_CD(SNCT Proc; LOINC) Fully. Specified. Name_char 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 Value. Flag_CD Observation_Blob Valcode_CD Obs_Concept 1 Observation_fact. N 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 Value. Flag_CD Observation_Blob Valcode_CD PK Concept_Path Concept_CD(SNCT Obs; LOINC) Fully. Specified. Name_char PK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD Encounter. Type_CD Service. Type_CD Observer_dimension PK Observer_Path Observer_CD Name_char Role_CD Obs_Concept. N PK Concept_Path Concept_CD(SNCT Obs; LOINC) Fully. Specified. Name_char
Allergy List Patient_dimension PK Patient_num Birth_date Death_date Vital_status_CD Age_num Gender_CD Race_CD Ethnicity_CD Allergy. List_fact Sevmodifier_dimension 255604002|mild| 6736007|moderate| 24484000|severe| 399166001|fatal| 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 Value. Flag_CD Observation_Blob Allergy. List_dimension PK Concept_Path Concept_CD(<<418038007) Fully. Specified. Name_char 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 Value. Flag_CD Observation_Blob Allergen_dimension PK Concept_Path Concept_CD(<<406455002 <<410942007) Fully. Specified. Name_char Visit_dimension PK Encounter_num Start_datetime End_datetime Active_status_CD Location_CD Encounter. Type_CD Service. Type_CD Allergy. Reaction_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 Value. Flag_CD Observation_Blob Reaction_dimension Observer_dimension PK Observer_Path Observer_CD Name_char Role_CD PK Concept_Path Concept_CD(<<404684003) Fully. Specified. Name_char
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