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Awaiting Approval

1. Purpose​

This SOP provides guidelines for the mandatory Tier 1 data elements that all CHoRUS sites must provide as the minimal list of elements to be contributed. It defines the essential clinical data requirements organized by domain and subdomain, along with associated concept set identifiers and recommendations for OMOP CDM implementation. This ensures standardized data collection across all participating sites while supporting comprehensive phenotype-based research capabilities.

2. Scope​

This SOP applies to all CHoRUS participating sites, data engineers, and clinical data managers responsible for implementing the mandatory minimum dataset. It covers all essential domains from laboratory values through imaging data, ensuring consistent data availability for cross-site research and analysis.

3. Definitions​

  • Tier 1 Data Elements: The mandatory minimal list of data elements that all sites must provide to participate in CHoRUS.
  • Concept Set ID: A collection of admissible OMOP concept IDs to represent corresponding data elements, maintained in the CHoRUS concept inventory.
  • Domain: High-level categorization of clinical data (Laboratory, Procedures, Drugs, etc.) as defined by OMOP CDM.
  • Subdomain: More granular categorization within domains (Blood Chemistry, Hematology, etc.).
  • B2AI OHDSI Atlas: The central repository for CHoRUS concept sets available for collaborative development and maintenance.

4. Roles and Responsibilities​

  • Site Data Manager: Ensures all Tier 1 elements are captured and properly mapped to specified concept sets.
  • Data Engineer: Implements ETL processes to extract and transform Tier 1 elements according to OMOP CDM specifications.
  • Clinical Subject Matter Expert: Validates clinical appropriateness of concept mappings and data element definitions.
  • Quality Control Analyst: Verifies completeness and accuracy of Tier 1 element implementation across all sites.

5. Materials Needed​

  • Access to CHoRUS Concept Set Inventory and B2AI OHDSI Atlas.
  • OMOP CDM vocabulary and concept relationship tables.
  • Site-specific EHR data dictionaries and source system documentation.
  • Concept set validation tools and mapping documentation.

6. Procedures​

6.1. Mandatory OMOP Tables​

  1. Core Person and Visit Information: Ensure completeness of foundational tables:
    • PERSON table: Date/time of birth, biological sex, ethnicity
    • DEATH table: Datetime of death (when applicable)
    • OBSERVATION_PERIOD table: Data availability periods
    • VISIT_OCCURRENCE and VISIT_DETAIL tables: Encounter information

6.2. Laboratory Domain Implementation​

  1. Blood Chemistry Subdomain (MEASUREMENT domain):

    • Sodium (Concept Set ID: 7, 8): Include standard measurement concepts for serum, plasma, or blood sodium, excluding other specimen types
    • Potassium (Concept Set ID: 19): Include standard measurement concepts for serum, plasma, or blood potassium
    • Creatinine (Concept Set ID: 26): Serum/plasma creatinine measurements
    • BUN (Concept Set ID: 27): Blood urea nitrogen measurements
    • Glucose (including POC): Point-of-care glucose will have different concept IDs than standard lab glucose
    • Total Bilirubin (Concept Set ID: 28): Serum/plasma total bilirubin
    • Direct (Conjugated) Bilirubin (Concept Set ID: 29): Measured in serum/plasma, indicates cholestasis or hepatobiliary obstruction
    • Indirect Bilirubin (Concept Set ID: 30): Calculated as Total - Direct bilirubin
    • Lactate (Concept Set ID: 31): Include lactate from blood gases
    • Troponin (Concept Set ID: 54): Cardiac biomarker
    • D-dimers (Concept Set ID: 55): Coagulation marker
    • Ammonia (Concept Set ID: 56): Hepatic function marker
    • Serum Ketones (Concept Set ID: 57): Metabolic marker
    • CPK (CK) (Concept Set ID: 58): Creatine phosphokinase
    • Ferritin (Concept Set ID: 60): Major inflammatory marker in pediatrics/neonates
    • CRP (Concept Set ID: 60): C-reactive protein inflammatory marker

  2. Hematology Subdomain:

    • WBC Count/Leukocyte (Concept Set ID: 61): White blood cell count
    • Hemoglobin (Concept Set ID: 63): Hemoglobin concentration
    • Hematocrit (Concept Set ID: 64): Packed cell volume
    • Platelets (Concept Set ID: 65): Platelet count
    • Differential Counts: Not required but should be included if available

  3. Coagulation Subdomain:

    • INR (Concept Set ID: 66): International normalized ratio
    • PTT (Concept Set ID: 67): Partial thromboplastin time
    • Fibrinogen (Concept Set ID: 68): Coagulation factor

  4. Blood Gas Analysis:

    • Include all sources: arterial, venous, capillary, central venous
    • PO2: Arterial (69), Venous (73), Capillary (76)
    • PCO2: Arterial (70), Venous (77), Capillary (78)
    • pH: Arterial (71), Venous (75)
    • SaO2: Arterial (72), Venous (74), Capillary (79), Central Venous (90)

6.3. Microbiology Domain​

  1. Culture Results: Follow specific microbiology SOP
    • Specimen Collection (Concept Set ID: 81): Include collection/reporting dates, negative cultures
    • Specimen Site (Concept Set ID: 82): Blood, CSF, urine, etc.
    • Results (Concept Set ID: 83, 85): Positive/negative/specific results, titers, PCR
    • Susceptibility (Concept Set ID: 84): Antibiotic sensitivity testing

6.4. Procedures and Interventions​

  1. Radiology Procedures (PROCEDURE_OCCURRENCE table):

    • Chest Radiographs, CT, MRI (Concept Set ID: 86, 87, 88, 89)
    • EKG, EEG, US Head (neonates): Include procedures and associated reports

  2. Critical Care Procedures:

    • Mechanical Ventilation (Concept Set ID: 17)
    • Tracheal Intubation (Concept Set ID: 18)
    • Tracheostomy, KRT, ECMO: All forms of renal replacement therapy
    • Therapeutic Hypothermia (neonates, Concept Set ID: 91)
    • Phototherapy (neonates, Concept Set ID: 20)

6.5. Medications (DRUG_EXPOSURE table)​

  1. Critical Care Medications: Include dose/infusion rate as relevant

    • Vasopressors, Anticoagulants, Inotropes, Diuretics
    • Sedatives, Analgesics, Paralytics, Antimicrobials
    • Chemotherapy, Immunosuppression (including steroids)
    • Anticonvulsants

  2. Specialized Medications:

    • Surfactant (neonates)
    • Caffeine (neonates)
    • Albumin

6.6. Flowsheet and Vital Signs (MEASUREMENT/OBSERVATION tables)​

  1. Vital Signs:

    • Blood Pressure: Invasive and non-invasive (systolic, diastolic, mean), include central venous pressure
    • Heart Rate/Pulse, Respiratory Rate, Pulse Oximetry (SpO2), Temperature

  2. Pediatric/Neonatal Assessments:

    • APGAR Scores: 1-minute (45), 5-minute (44), 10-minute (43)
    • Biometrics: Weight (kg), Height (cm), Head circumference (90), Length (neonates/pediatrics)
    • Gestational Age (weeks, 50), Birth Weight (grams, 92)

  3. Clinical Assessments:

    • Delirium Scores: CAM-ICU or similar (10), Pediatric scores (CAPD, pCAM-ICU, psCAM-ICU)
    • Agitation Scores: RASS (9), Pediatric State Behavior Scale
    • Pain Scores: Neonatal NPASS (39), Glasgow (13)
    • Neonatal Assessments: Abstinence syndrome (37), Reflexes - Suck (35), Grasp (36), Moro (42)

6.7. Mechanical Ventilation Data​

  1. Ventilator Settings (OBSERVATION table):

    • Ventilation Modes: AC-VC, PC, PRVC, SIMV, High frequency, PS/CPAP, VS, Blow-by
    • FIO2 Setting (16): Fraction in range [0.21, 1.0]
    • PEEP Setting (15), Tidal Volume Setting
    • Other Settings: Inspiratory time, flow, pressure support

  2. Ventilator Measurements:

    • Total Rate, Minute Ventilation (12), Peak Pressure, Mean Airway Pressure (14)

  3. Non-Invasive Ventilation:

    • NIV Settings: Rate, CPAP, PS support, EPAP, IPAP (15)
    • NIV Modes: CPAP, BiPAP, other

6.8. Input and Output Tracking​

  1. Intake Measurements:

    • IV Fluids: Maintenance, bolus, drug infusions (cc/hr)
    • Blood Products: Whole blood, RBC, platelets, plasma, cryoprecipitate (cc)
    • Other Intakes: Oral, GI feeds, infant feeds

  2. Output Measurements:

    • Urine Output (11): All forms (cc)
    • Drainage: Various drain types (cc)
    • Blood Loss, Dialysis (CKRT, all forms), Other Output (cc)

6.9. Clinical Documentation​

  1. Notes (NOTE table):

    • Mandatory: H&P, Progress notes, Discharge summary
    • Desirable: Operative reports, rapid response, consults, ancillary services

  2. Reports:

    • Mandatory: Radiology, EEG, ECG, Echo
    • Desirable: US, PFTs, other diagnostic reports

6.10. Conditions and Code Status​

  1. Diagnostic Information (CONDITION_OCCURRENCE table):
    • All Diagnostic Codes, All Problems
    • Code Status: Full code, comfort measures, DNR, DNI, other limitations

6.11. Physiological Monitoring Data​

  1. Waveform Data: Follow specific SOP

    • Monitor Numerics: All available parameters
    • EEG Data: Persyst format
    • ECG, PPG: Other monitor waveforms

  2. Imaging Data: Follow specific SOP

    • Radiology: CXR, CT Head, CTAP, CT-angio, MRI
    • Other Imaging: Abdominal, trauma-related studies

7. Quality Control (QC) Procedures​

  • Completeness Validation: Verify all Tier 1 elements are present for each patient encounter
  • Concept Set Compliance: Ensure all data elements map to specified concept set IDs
  • Domain Verification: Confirm appropriate OMOP domain placement for each element type
  • Temporal Consistency: Validate logical time relationships between related measurements
  • Cross-Domain Linkage: Verify proper linkage between procedures, medications, and outcomes

8. Documentation and Storage​

  • Maintain comprehensive mapping documentation between source systems and Tier 1 concept sets
  • Document any site-specific variations or limitations in Tier 1 element capture
  • Store validation results and completeness metrics for ongoing quality monitoring
  • Maintain change logs for concept set updates and implementation modifications

9. Deviations from the SOP​

  • Any inability to provide mandatory Tier 1 elements must be documented with clinical and technical justifications
  • Alternative concept mappings require approval through CHoRUS Standards governance
  • Site-specific limitations must be clearly documented in data submission metadata

10. Revision History​

VersionDateDescription
1.02025-09-01Initial version based on Tier 1 phenotype requirements document