Data Dictionary

The C19HCC Data Dictionary anchors the patient cohort descriptions and other definitions. The classes and elements are not expected to be literally presented in any EHR. It will require manual effort to map the EHR to the cohort definitions. The classes and elements listed here align to standard models such as FHIR and OHDSI CDM, borrowing concepts from both.

Version 2.80

Last updated: May 7, 2020
11 files > 69 fields
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Root (root)

2 Fields
Metadata applicable to all data elements.
Field & Description
Type
Permissible Values
Notes & Mappings
reported_date
The date or date-time the observation is reported.
DATE
patient_id
Unique identifier assigned to the patient.
ID
FHIR: Patient.identifier, PCORnet: Demographics.patid, OHDSI CDM: Person.person_id, Sentinel: Demographic.PatID

Patient (patient)

5 Fields
The collection of data elements with demographic information about a patient.
Field & Description
Type
Permissible Values
Notes & Mappings
date_of_birth
The actual or approximate date of birth.
DATE
administrative_gender
The gender that the patient is considered to have for administration and record keeping purposes.
CODE

Male

Female

Other

Unknown

Codes must align with FHIR Administrative Gender value set (http://hl7.org/fhir/ValueSet/administrative-gender). FHIR: Patient.gender, OHDSI CDM: Person.gender_concept_id, PCORnet: Demographics.sex, Sentinel: Demographic.Sex, I2B2: Demographics.sex
race
Concepts classifying the person into a named category of humans sharing common history, traits, geographical origin or nationality. The race codes used to represent these concepts are based upon the CDC Race and Ethnicity Code Set Version 1.0.
CODE

American Indian or Alaska Native

Asian

Black or African American

Native Hawaiian or Other Pacific Islander

White

2 more
Codes from http://hl7.org/fhir/us/core/ValueSet/omb-race-category. FHIR: Patient.extension: us-core-race, PCORnet: Demographics.race, OHDSI CDM: Person.race_concept_id, Sentinel: Demographic.Race, I2B2: Demographics.Race
ethnicity
Concepts classifying the person into a named category of humans sharing common history, traits, geographical origin or nationality. The ethnicity codes used to represent these concepts are based upon the CDC Race and Ethnicity Code Set Version 1.0.
CODE

Hispanic or Latino

Non Hispanic or Latino

Codes from http://hl7.org/fhir/us/core/ValueSet/omb-ethnicity-category. FHIR: Patient.extension: us-core-ethnicity, PCORnet: Demographics.hispanic, OHDSI CDM: Person.ethnicity_concept_id, Sentinel: Demographic.Hispanic, I2B2: Demographics.Hispanic
zip_code
Zip code of the primary residence of the patient.
TEXT
Values must meet the regular expression
Five digit zip code is acceptable. FHIR: Patient.address, OHDSI CDM: Person.location_id, Sentinel: Demographic.Zip

Vital Status (Vital_status)

3 Fields
An indicator of whether the patient is alive or dead.
Field & Description
Type
Permissible Values
Notes & Mappings
vital_status
Donor's last known state of living or deceased.
CODE

Alive

Deceased

Unknown

FHIR: Patient.deceasedBoolean, PCORnet: Death.patid, Death_cause.patid, OHDSI CDM: DEATH.person_id (deprecated in CDM 6.0), VISIT_DETAIL.DISCHARGE_TO_CONCEPT_ID = 4216643 'Patient died', OBSERVATION_TYPE_CONCEPT_ID = 44818516 (EHR discharge status 'Expired').
cause_of_death
Indicates the cause of a patient's death.
CODE

ICD-10 Code

SNOMED-CT code

Cause of death is only required to be submitted if the patient is deceased. Mortality coding of COVID-19 with ICD-10 see: https://www.who.int/classifications/icd/COVID-19-coding-icd10.pdf?ua=1. FHIR: VRDR Cause of Death Condition profile; FHIR: AdverseEvent.suspectedEntity.causality.Extension (Proposed Name: cause-code : CodeableConcept), PCORnet: Death_cause.death_cause, Death_cause.death_cause_code, OHDSI CDM: Death.death_type_concept_id, Death.cause_concept_id.
date_of_death
Indicates the actual or approximate date of a patient's death.
DATE
Date of death is only required to be submitted if the patient is deceased. FHIR: Patient.deceasedDateTime, VRDR Death Date profile, AdverseEvent.date, PCORnet: Death.death_date, OHDSI CDM: Death.death_date

Patient PII (patient_PII)

6 Fields
Personally identifiable information about a patient.
Field & Description
Type
Permissible Values
Notes & Mappings
family_name
The part of a name that links to the genealogy.
TEXT
FHIR: Patient.name.family. Patient PII not reported in other systems.
given_name(s)
Given names (not always 'first'). Includes middle names.
TEXT
FHIR: Patient.name.given. Patient PII not reported in other systems.
address_line
This component contains the house number, apartment number, street name, street direction, P.O. Box number, delivery hints, and similar address information.
TEXT
FHIR: Patient.address.line. Patient PII not reported in other systems.
address_city
The name of the city, town, suburb, village or other community or delivery center.
TEXT
FHIR: Patient.address.city. Patient PII not reported in other systems.
address_state
US 2 letter state code.
TEXT
FHIR: Patient.address.state. Patient PII not reported in other systems.
primary_phone_number
Preferred phone number for the patient.
TEXT
FHIR: Patient.contact.telecom. Patient PII not reported in other systems.

Condition (condition)

6 Fields
The collection of data elements related to a condition. A condition can be either a diagnosis or part of an ongoing problem list.
Field & Description
Type
Permissible Values
Notes & Mappings
condition_id
Unique identifier assigned to this instance of condition in the patient.
ID
FHIR: Condition.id, PCORnet: Diagnosis.diagnosisid, Condition.conditionid, OHDSI CDM: Condition_occurrence.condition_occurrence_id
code
The code to represent the condition, diagnosis or problem.
CODE

ICD-10-CM code

SNOMED CT disorder code

This field accepts either ICD-10-CM or SNOMED-CT disorder codes. FHIR: Condition.code, PCORnet: Diagnosis.dx, Diagnosis.dx_type, Condition.condition, Condition.condition_type, OHDSI CDM: Condition_occurrence.condition_concept_id, I2B2: Diagnosis.DIAGNOSIS_CODE, Diagnosis.DIAGNOSIS_CODING_SYSTEM, Diagnosis.DIAGNOSIS_CODING_SYSTEM_VERSION.
category
Condition category which distinguishes between a diagnosis or a problem.
CODE

problem-list-item

encounter-diagnosis

Include all codes defined in http://terminology.hl7.org/CodeSystem/condition-category. FHIR: Condition.category, I2B2: Diagnosis.DIAGNOSIS_SOURCE
onset_date
An estimate or actual date that the patient reported experiencing the condition.
DATE
FHIR: Condition.onsetDateTime, PCORnet: Condition.onset_date, I2B2: Diagnosis.DIAGNOSIS_DATE
verification_date
Date when condition was confirmed by positive test, imaging, biopsy, or other method.
DATE
TBD
clinical_status
The clinical status of the condition. (Reference source: FHIR Condition clinical status from http://hl7.org/fhir/condition-definitions.html#Condition.clinicalStatus).
CODE

active

recurrence

relapse

inactive

remission

1 more
The clinical status terms are described at http://hl7.org/fhir/valueset-condition-clinical.html. FHIR: Condition.clinicalStatus, PCORnet: Condition.condition_status, OHDSI CDM: Condition_occurrence.condition_status_concept_id

Med Exposure (med_exposure)

8 Fields
An instance of a medication or substance introduced into the body. Medication exposures are indicated by a variety of records: medication orders, medication administrations, medication lists, and patient-reported medication statements.
Field & Description
Type
Permissible Values
Notes & Mappings
med_id
Unique identifier assigned to the medication exposure episode.
ID
code
The code to represent the medication that was administered.
CODE

RxNorm code: http://www.nlm.nih.gov/research/umls/rxnorm

NDC code: http://hl7.org/fhir/sid/ndc

Medications can be reported in NDC or RxNorm. For NDC, the product code or package code is acceptable. For RxNorm, the ingredient (IN) or multiple ingredient (MIN) codes are preferred over the brand codes or combination (Ingredient + Strength (SCDC), Ingredient + Dose Form (SCDF), etc.). FHIR: MedicationDispense.medicationCodeableConcept, MedicationRequest.medicationCodeableConcept, MedicationStatement.medicationCodeableConcept, PCORnet: Prescribing.rxnorm_cui, OHDSI CDM: Drug_exposure.drug_concept_id, Drug_exposure.drug_type_concept_id, I2B2: Medication.MEDICATION_ CLASSIFICATION_SYSTEM, Medication.MEDICATION_ CODING_SYSTEM, Medication.MEDICATION_ CLASSIFICATION_SYSTEM_VERSION, Medication.MEDICATION_ CLASSIFICATION_SYSTEM, Medication.MEDICATION_CODE, Medication.MEDICATION_CODING_SYSTEM_VERSION, Medication.RAW_ MEDICATION_CODE
med_dose_quantity
The amount of the medication given at one administration event.
QUANTITY
FHIR: MedicationRequest(MedicationDispense).dosageInstruction.doseAndRate.dose[x], MedicationStatement.dosage.doseAndRate.dose[x], PCORnet: Prescribing.rx_dose_form, Prescribing.rx_dose_ordered, Prescribing.rx_dose_ordered_unit, OHDSI CDM: Drug_exposure.quantity
med_dose_units
Unit of measure for the dose quantity of the administered medication.
CODE

UCUM code

Nomenclature conforms to the Unified Code for Units of Measure (UCUM): https://unitsofmeasure.org/trac. FHIR: MedicationRequest(MedicationDispense).dosageInstruction.doseAndRate.doseQuantity.system/code, PCORNet: Prescribing.rx._dose_ordered_unit
med_route
The path of the substance into the body for the administered medication.
CODE

Include codes from http://snomed.info/sct where concept is-a 284009009 (Route of administration values)

FHIR: MedicationDispense(MedicationRequest).dosageInstruction.route, PCORnet: Dispensing.dispense_route, PCORnet: Prescribing.rx_route, OHDSI CDM: Drug_exposure.route_concept_id, I2B2: Medication.RAW_MEDICATION_ROUTE
med_frequency
The timing for the frequency that the medication was taken.
TEXT
Frequency should be reported as a string instead of a complex data structure to simplify the collection of data. FHIR: MedicationRequest.dosageInstruction.timing, PCORnet: Prescribing.rx_frequency
med_start_date
The date when the medication was started.
DATE
FHIR: MedicationDispense.whenHandedOver, MedicationStatement.effectivePeriod.start, PCORnet: Dispensing.dispense_date, OHDSI CDM: Drug_exposure.drug_exposure_start_date, Drug_exposure.drug_exposure_start_datetime
med_stop_date
The date when the medication as administered to the patient.
DATE
If the stop date is not provided, it is assumed the medication is ongoing at the time of the report. FHIR: MedicationStatement.effectivePeriod.end, OHDSI CDM: Drug_exposure.drug_exposure_end_date, Drug_exposure.drug_exposure_end_datetime. May be calculated from FHIR: MedicationStatement.basedOn(MedicationRequest).dispenseRequest.expectedSupplyDuration, OHDSI CDM: Drug_exposure.days_supply

Procedure (procedure)

5 Fields
An action that was performed on or for a patient. This can be a physical intervention like an operation, or less invasive services such as counseling.
Field & Description
Type
Permissible Values
Notes & Mappings
procedure_id
Unique identifier assigned to the procedure occurrence.
ID
FHIR: Procedure.id, PCORnet: Procedures.proceduresid, OHDSI CDM: Device_exposure.device_exposure_id, Procedure_occurrence.procedure_occurrence_id
code
The code representing the procedure. A procedure is an action performed on a patient, including diagnostic tests, therapies - such as respiratory therapy, surgeries, and other clinical interventions.
CODE
SNOMED CT (preferred), ICD-10-CM (preferred) or HCPCS (alternative). FHIR: Procedure.code, PCORnet: Procedures.px, Procedures.px_type, OHDSI CDM: Procedure_occurrence.procedure_concept_id, I2B2: Procedure.PROCEDURE_ CODING_SYSTEM, Procedure.PROCEDURE_CODE, Procedure.PROCEDURE_CODING_SYSTEM_VERSION
status
The status of the procedure in terms of workflow.
CODE

in-progress

aborted

completed

entered-in-error

start_date
The date and time the procedure started.
DATE
FHIR: Procedure.performedDateTime, Procedure.performedPeriod.start, PCORnet: Procedures.px_date, OHDSI CDM: Procedure_occurrence.procedure_date, Procedure_occurrence.procedure_datetime, I2B2: Procedure.PROCEDURE_DATE
end_date
The date and time the procedure ended.
DATE
FHIR: Procedure.performedPeriod.end, OHDSI CDM: Device_exposure.device_exposure_end_date, Device_exposure.device_exposure_end_datetime

Lab Result (lab_result)

8 Fields
An individual laboratory test and result value
Field & Description
Type
Permissible Values
Notes & Mappings
lab_result_id
Unique identifier of the lab test.
ID
FHIR: Observation.id, PCORnet: Lab_result_cm.lab_result_cm_id, OHDSI CDM: Measurement.measurement_id, Observation.observation_id
code
The code identifying the type of lab test performed.
CODE

LOINC code

LOINC is preferred as the coding system for the lab test. In cases where there is a no LOINC code immediately available, a local test code would be accepted provided that there is a code system listing where the code originated. FHIR: Observation.code, PCORnet: Lab_result_cm.lab_loinc, Lab_result_cm.raw_lab_name, OHDSI CDM: Measurement.measurement_concept_id, Observation.observation_concept_id, I2B2: Laboratory_test.RAW_PANEL, Laboratory_test.LAB_ CLASSIFICATION _SYSTEM_VERSION, Laboratory_test.LAB_ CLASSIFICATION_SYSTEM, Laboratory_test.LAB_ CODING_SYSTEM, Laboratory_test.LAB_CODE, Laboratory_test.LAB_CODING_SYSTEM_VERSION, Laboratory_test.RAW_LAB_CODE
relevant_dateTime
The date or dateTime when the specimen was collected.
DATETIME
FHIR: Observation.effectiveDateTime, Observation.basedOn(ServiceRequest).occurrenceDateTime, PCORnet: Lab_result_cm.lab_order_date, OHDSI CDM: Measurement.measurement_date, Measurement.measurement_datetime, Observation.observation_date, Observation.observation_datetime
result_dateTime
The date or dateTime when the result was reported.
DATETIME
FHIR: Observation.issued, PCORnet: Lab_result_cm.result_date, Lab_result_cm.result_time
result_code
The value associated with a lab result, represented as a code.
CODE
FHIR: Observation.valueCodeableConcept, PCORnet: Lab_result_cm.result_snomed, OHDSI CDM: Measurement.value_as_concept_id, Observation.value_as_concept_id, I2B2: Laboratory_test.RESULT_QUALITATIVE
result_quantity
The value associated with a lab result, represented as a number. The number can be either an integer or a float.
QUANTITY
FHIR: Observation.valueQuantity, PCORnet: Lab_result_cm.result_qual, Lab_result_cm.result_num, Lab_result_cm.result_modifier,Lab_result_cm.raw_result, Measurement.value_as_number, Observation.value_as_number, I2B2: Laboratory_test.RAW_RESULT, Laboratory_test.RESULT_MODIFIER, Laboratory_test.RESULT_NUMERICAL
result_units
Unit of measure for the associated with the lab result quantity.
CODE

UCUM code

Nomenclature conforms to the Unified Code for Units of Measure (UCUM): https://unitsofmeasure.org/trac. FHIR: Observation.valueQuantity.system/codes PCORnet: Lab_result_cm.result_unit, OHDSI CDM: Measurement.unit_concept_id, I2B2: Laboratory_test.RAW_UNIT, Laboratory_test.RESULT_UNIT
lab_result_interpretation
An interpretation associated with the lab test result
CODE

Any of the codes specified in the http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation value set.

FHIR: Observation.interpretation, PCORnet: Lab_result_cm.abn_ind, I2B2: Laboratory_test.ABNORMAL_RESULT_INDICATOR

Encounter (encounter)

10 Fields
Data elements associated with an encounter at a health care facility, such as an ambulatory visit, an emergency department visit, or a hospitalization.
Field & Description
Type
Permissible Values
Notes & Mappings
encounter_id
A unique identifier for the encounter.
ID
FHIR: Encounter.id, PCORnet: Encounter.encounterid, OHDSI CDM: Visit_occurrence.visit_occurrence_id, Sentinel: Encounter.EncounterID
facility_id
Unique identifier of the facility providing the encounter.
ID
FHIR: Location.id, OHDSI CDM: Care_site.care_site_id, Location.location_id
encounter_class
A classification of the encounter, e.g. ambulatory, emergency or inpatient
CODE

AMB (ambulatory)

EMER (emergency)

FLD (field)

HH (home health)

IMP (inpatient encounter)

6 more
Permissible values descriptions are available at http://hl7.org/fhir/v3/ActEncounterCode/vs.html. FHIR: Encounter.class, PCORnet: Encounter.enc_type, Sentinel: Encounter.EncType, I2B2: Procedure.VISIT.VISIT_TYPE
admission_date
The date the patient was admitted for the encounter
DATE
FHIR: Encounter.period.start, PCORnet: Encounter.admit_date, Encounter.admit_time, OHDSI CDM: Visit_occurrence.visit_start_date, Visit_occurrence.visit_start_datetime, Sentinel: Encounter.ADATE, I2B2: Procedure.VISIT.ADMIT_DATE
admission_source
The type of location the patient originated from.
CODE

Any of the codes specified in the http://terminology.hl7.org/CodeSystem/admit-source value set

Definitions for the permissible values are available at http://hl7.org/fhir/codesystem-encounter-admit-source.html. FHIR: Encounter.hospitalization.admitSource or Encounter.hospitalization.origin(location).type, PCORnet: Encounter.admitting_source, OHDSI CDM: Visit_occurrence.admitting_source_concept_id, Sentinel: Encounter.Admitting_Source
discharge_date
The date the patient was discharged from the encounter
DATE
FHIR: Encounter.period.end, PCORnet: Encounter.discharge_date, Encounter.discharge_time, OHDSI CDM: Visit_occurrence.visit_end_date, Visit_occurrence.visit_end_datetime, Sentinel: Encounter.DDATE, I2B2: Procedure.VISIT.DISCHARGE_DATE
discharge_disposition
Categorization of the status of the patient at discharge according to the type of location the patient was discharged to.
CODE

home (Home)

alt-home (Alternative home)

other-hcf (Other healthcare facility)

hosp (Hospice)

long (Long-term care)

6 more
Definitions for the permissible values are available at https://www.hl7.org/fhir/valueset-encounter-discharge-disposition.html. FHIR: Encounter.extension (Proposed Name: discharge-disposition: CodeableConcept), PCORnet: Encounter.discharge_disposition, Sentinel: Encounter.Discharge_Disposition
initial_diagnosis
The initial working diagnosis (also known as 'chief complaint') first entered into the EHR
CODE

ICD-10-CM code

SNOMED CT code

FHIR: Encounter.diagnosis.condition (Role = CC), OHDSI CDM: Condition_occurrence with condition_status_concept_id = 4033240, PCORnet: DIAGNOSIS.DX_SOURCE (IN)
admitting_diagnosis
The main diagnosis code used to admit the patient.
CODE

ICD-10-CM code

SNOMED CT disorder code

An admitting diagnosis is only expected to be available for inpatient encounters. FHIR: Encounter.diagnosis.condition (Role = AD),OHDSI CDM: Condition_occurrence with condition_status_concept_id = 4203942, PCORnet: DIAGNOSIS with DX_SOURCE=AD
discharge_diagnosis
The final diagnosis determined to be the main cause for the hospitalization after all testing, surgery, and workup are complete.
CODE

ICD-10-CM code

SNOMED CT disorder code

Discharge diagnosis is only expected to be available for inpatient encounters that have been completed. FHIR: Encounter.diagnosis.condition (Role = DD), OHDSI CDM: Condition_occurrence with condition_status_concept_id = 4230359, PCORnet: DIAGNOSIS with DX_SOURCE=DI

Encounter Detail (encounter_detail)

6 Fields
Department, unit or setting the patient visits during the course of an inpatient encounter, such as emergency department or intensive care unit.
Field & Description
Type
Permissible Values
Notes & Mappings
encounter_id
A unique identifier for the encounter.
ID
OHDSI CDM: visit_detail_parent_id
encounter_detail_id
A unique identifier for the instance of encounter setting.
ID
OHDSI CDM: visit_detail_id
type
The type of setting according to its function/purpose
CODE

Code from http://terminology.hl7.org/ValueSet/v3-ServiceDeliveryLocationRoleType value set.

Definitions for the permissible values for setting type are available at http://hl7.org/fhir/v3/ServiceDeliveryLocationRoleType/vs.html. OHDSI CDM: visit_detail_type_concept_id
arrival_date
The date the patient arrived at the setting.
DATE
OHDSI CDM: visit_detail_start_date, visit_detail_start_datetime
departure_date
The date the patient departed the setting.
DATE
OHDSI CDM: visit_detail_end_date, visit_detail_end_datetime
length of stay
The length of time a patient spent in the setting.
QUANTITY
Can be derived from arrival and departure dates.

Patient Observation (patient_observation)

10 Fields
Clinical information obtained through examination, assessment, survey, or questioning, including vital signs.
Field & Description
Type
Permissible Values
Notes & Mappings
observation_id
Unique identifier of the observation.
ID
code
The code identifying the type of observation.
CODE

LOINC code

LOINC is preferred as the coding system for the observation. In cases where there is a no LOINC code immediately available, a local test code would be accepted provided that there is a code system listing where the code originated. FHIR: Observation.code, PCORnet: specific VITAL table elements, PRO_CM: CM_LOINC, OHDSI CDM: Measurement.measurement_concept_id, Observation.observation_concept_id
observation_datetime
The date-time of the observation, if the observation is made at a specific time.
DATETIME
Either the observation_datetime or the observation_period_start should be reported, but not both. FHIR: Observation.effectiveDateTime.start, PCORnet: Vital.measure_date, Vital.measure_time, OMOP: Measurement.measurement_date, Measurement.measurement_datetime, Observation.observation_date, Observation.observation_datetime
observation_period_start
The date or date-time marking the beginning of the clinically-relevant time period of the observation.
DATETIME
Either the observation_datetime or the observation_period_start should be reported, but not both.
observation_period_end
The date or date-time marking end of the observation period. If the observation_period_start is reported and the observation_period_end is not reported, the observation is assumed to be ongoing at the time of reporting.
DATETIME
result_string
The value associated with the observation, represented as a text.
TEXT
A textual description of the observation result. A code is preferred if available.
result_code
The value associated with the observation, represented as a code.
CODE
result_quantity
The value associated with a lab result, represented as a number. The number can be either an integer or a float.
QUANTITY
result_units
Unit of measure for the associated with the lab result quantity.
CODE

UCUM code

Nomenclature conforms to the Unified Code for Units of Measure (UCUM): https://unitsofmeasure.org/trac. FHIR: Observation.valueQuantity.system/codes PCORnet: OHDSI CDM: Measurement.unit_concept_id
result_interpretation
An interpretation associated with the observation
CODE

Any of the codes specified in the http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation value set.

FHIR: Observation.interpretation

  • root
    2 fields
    • patient
      5 fields
      • Vital_status
        3 fields
      • patient_PII
        6 fields
      • condition
        6 fields
      • med_exposure
        8 fields
      • procedure
        5 fields
      • lab_result
        8 fields
      • encounter
        10 fields
        • encounter_detail
          6 fields
      • patient_observation
        10 fields

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