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Mimic Ed Fhir Mappings

MIMIC-ED to FHIR Mappings

The MIMIC-ED database was converted into FHIR. The tables from MIMIC-ED were each mapped to a one or more resources. The diagram below depicts these mappings:

Custom profiles were created to house the tables coming into FHIR. This was necessary to handle the unique terminology coming from MIMIC-ED. In the following sections you will see tables detailing the mapping from each MIMIC-ED table to these MIMIC-FHIR profiles.

Condition

One Condition resource per diagnosis (row in diagnosis table).

MIMIC-ED Table	MIMIC-ED Data Element	FHIR Data Element	FHIR Profile	Notes
diagnosis	stay_id, seq_num, icd_code	Condition.id	MimicCondition	Id made up of concatenation of stay_id, seq_num, and icd_code, converted to UUID5
diagnosis	icd_version	Condition.code.CodeableConcept.system	MimicCondition	If ‘9’ URI of ICD9 if ‘10’ URI of ICD10 (MIMIC code systems)
diagnosis	icd_code	Condition.code.CodeableConcept.code	MimicCondition
diagnosis	subject_id	Condition.subject	MimicCondition	Links to a MimicPatient with corresponding identifier
diagnosis	stay_id	Condition.encounter	MimicCondition	Links to a MimicEncounter with corresponding identifier

• Condition.category is fixed to ‘encounter-diagnosis’ (Encounter Diagnosis) for all MIMIC conditions

Encounter

One Encounter resource per stay_id (i.e., per ED visit / per row in the edstays table).

MIMIC-ED Table	MIMIC-ED Data Element	FHIR Data Element	FHIR Profile	Notes
edstays	stay_id	Encounter.identifier:ED_ID	MimicEncounter	This is a sliced element, ED identifier is captured in the ED_ID slice.
edstays	subject_id	Encounter.subject	MimicEncounter	Links to a MimicPatient with corresponding identifier
edstays	intime	Encounter.period.start	MimicEncounter
edstays	outtime	Encounter.period.end	MimicEncounter
edstays	arrival_transport	Encounter.hospitalization.admitSource	MimicEncounter	MIMIC code system
edstays	disposition	Encounter.hospitalization.dischargeDisposition	MimicEncounter	MIMIC code system

• Encounter.status is fixed to ‘finished’ (Finished) for all MIMIC encounters
• Encounter.class should be ‘EMER’ (Emergency) for all MIMIC-ED encounters

MedicationDispense ED

One MedicationDispense resource per dispense in the pyxis table (ED medication dispensation). A dispense can consist of multiple rows with the same subject_id, stay_id, and charttime but multiple medication codes.

MIMIC-ED Table	MIMIC-ED Data Element	FHIR Data Element	FHIR Profile	Notes
pyxis	stay_id, med_rn, gsn_rn	MedicationDispense.id	MimicMedicationDispenseED	Concat MIMIC columns and convert to UUID5
pyxis	subject_id	MedicationDispense.subject	MimicMedicationDispenseED	Convert to UUID5
pyxis	stay_id	MedicationDispense.context	MimicMedicationDispenseED	Convert to UUID5
pyxis	gsn	MedicationDispense.medicationCodeableConcept.coding	MimicMedicationDispenseED	MIMIC code system
pyxis	name	MedicationDispense.medicationCodeableConcept.text	MimicMedicationDispenseED
pyxis	charttime	MedicationDispense.whenHandedOver	MimicMedicationDispenseED

• MedicationDispense.status is fixed to ‘unknown’ (Unknown)

MedicationStatement ED

One MedicationStatement resource per medication that was taken by a patient. A drug can have multiple etccode values (one per row, multiple rows) and are delineated by etc_rn.

MIMIC-ED Table	MIMIC-ED Data Element	FHIR Data Element	FHIR Profile	Notes
medrecon	stay_id, charttime, name, gsn, ndc	MedicationStatement.id	MimicMedicationStatementED	Concat elements to make unique id and convert to UUID5
medrecon	gsn	MedicationStatement.medicationCodeableConcept.coding:gsnCode	MimicMedicationStatementED	MIMIC code system. This is a sliced element, gsn codes are captured in the gsnCode slice.
medrecon	ndc	MedicationStatement.medicationCodeableConcept.coding:ndcCode	MimicMedicationStatementED	This is a sliced element, ndc codes are captured in the ndcCode slice.
medrecon	etccode	MedicationStatement.medicationCodeableConcept.coding:etccodeCode	MimicMedicationStatementED	MIMIC code system. This is a sliced element, etc codes are captured in the etccodeCode slice.
medrecon	name	MedicationStatement.medicationCodeableConcept.text	MimicMedicationStatementED
medrecon	subject_id	MedicationStatement.subject	MimicMedicationStatementED	Links to a MimicPatient with corresponding identifier
medrecon	stay_id	MedicationStatement.context	MimicMedicationStatementED	Links to a MimicEncounter with corresponding identifier
medrecon	charttime	MedicationStatement.dateAsserted	MimicMedicationStatementED

• MedicationStatement.status is fixed to ‘unknown’ (Unknown)
• MedicationStatement.medicationCodeableConcept.coding:etccodeCode has cardinality 0..*; allows multiple etc codes to be stored.

Observation ED

One Observation resource per single measurement from a row of the triage and vitalsign tables of MIMIC-ED. Only acuity, chiefcomplaint, rhythm, and pain.

MIMIC-ED Table	MIMIC-ED Data Element	FHIR Data Element	FHIR Profile	Notes
vitalsign	stay_id, charttime, key	Observation.id	MimicObservationED	Concat elements and convert to UUID5
vitalsign	rhythm	Observation.value[x]	MimicObservationED	If Observation captures rhythm
vitalsign	pain	Observation.value[x]	MimicObservationED	If Observation captures pain
vitalsign	subject_id	Observation.subject	MimicObservationED	Convert to UUID5
vitalsign	stay_id	Observation.encounter	MimicObservationED	Convert to UUID5
vitalsign	value	Observation.valueString	MimicObservationED
vitalsign	stay_id, charttime	Observation.partOf	MimicObservationED	Concat elements and convert to UUID5
triage	stay_id, intime, key	Observation.id	MimicObservationED	Concat elements and convert to UUID5
triage	acuity	Observation.value[x]	MimicObservationED	If Observation captures acuity
triage	chiefcomplaint	Observation.value[x]	MimicObservationED	If Observation captures chiefcomplaint
triage	pain	Observation.value[x]	MimicObservationED	If Observation captures pain
triage	subject_id	Observation.subject	MimicObservationED	Convert to UUID5
triage	stay_id	Observation.encounter	MimicObservationED	Convert to UUID5
triage	value	Observation.valueString	MimicObservationED
triage	stay_id, charttime	Observation.partOf	MimicObservationED	Concat elements and convert to UUID5

• Observation.status is fixed to ‘final’ (Final) for all MIMIC observations.
• Only for rhytm: Observation.category is fixed to ‘exam’ (Exam). In all other cases a category is absent.
• Observation.code corresponds to a LOINC code (from MIMIC-ED value set) for either an acuity, chiefcomplaint, or rhythm observation.
• Observation.value[x] has a 0..1 cardinality, hence only one measurement (acuity, rhythm, or chiefcomplaint) is captured in an Observation resource. When a value is missing, an Observation.dataAbsentReason is given (always ‘unknown’ (Unknown)).

Observation Vital Signs

One Observation resource per single measurement from a row of the triage and vitalsign tables of MIMIC-ED. Only temperature, heartrate, resprate, blood pressure sbp dbp, and o2sat.

MIMIC-ED Table	MIMIC-ED Data Element	FHIR Data Element	FHIR Profile	Notes
triage	stay_id	Observation.id	MimicObservationVitalSigns	Concat the stay_id with the vital sign name captured
triage	temperature	Observation.value[x]	MimicObservationVitalSigns	If observation is a temperature reading
triage	resprate	Observation.value[x]	MimicObservationVitalSigns	If observation is a respiratory rate
triage	heartrate	Observation.value[x]	MimicObservationVitalSigns	If observation is a heart rate reading
triage	o2sat	Observation.value[x]	MimicObservationVitalSigns	If observation is a oxygen saturation reading
triage	dbp	Observation.value[x]	MimicObservationVitalSigns	If observation is a blood pressure reading
triage	sbp, dbp	Observation.component.value[x]	MimicObservationVitalSigns	If Observation captures blood pressure (component for sbp and dbp).
triage	subject_id	Observation.subject	MimicObservationVitalSigns	Convert to UUID5
triage	stay_id	Observation.encounter	MimicObservationVitalSigns	Convert to UUID5
triage	stay_id	Observation.procedure	MimicObservationVitalSigns	Convert to UUID5
edstays	intime	Observation.effectiveDateTime	MimicObservationVitalSigns
vitalsign	stay_id, charttime	Observation.id	MimicObservationVitalSigns	Concat the stay_ida and charttime with the vital sign name captured, then convert to UUID5
vitalsign	temperature	Observation.value[x]	MimicObservationVitalSigns	If observation is a temperature reading
vitalsign	resprate	Observation.value[x]	MimicObservationVitalSigns	If observation is a respiratory rate
vitalsign	heartrate	Observation.value[x]	MimicObservationVitalSigns	If observation is a heart rate reading
vitalsign	o2sat	Observation.value[x]	MimicObservationVitalSigns	If observation is a oxygen saturation reading
vitalsign	dbp	Observation.value[x]	MimicObservationVitalSigns	If observation is a blood pressure reading
vitalsign	sbp, dbp	Observation.component.value[x]	MimicObservationVitalSigns	If Observation captures blood pressure (component for sbp and dbp).
vitalsign	subject_id	Observation.subject	MimicObservationVitalSigns	Convert to UUID5
vitalsign	stay_id	Observation.encounter	MimicObservationVitalSigns	Convert to UUID5
vitalsign	stay_id, charttime	Observation.procedure	MimicObservationVitalSigns	Concat elements and convert to UUID5

• Observation.status is fixed to ‘final’ (Final) for all MIMIC observations.
• Observation.category is fixed to ‘vital-signs’ (Vital Signs).
• Observation.code corresponds to a LOINC code (from MIMIC-ED value set) for either temperateure, respiratory rate, heart rate, oxygen saturation, or blood pressure.
• Observation.value[x] has a 0..1 cardinality, hence only one measurement (or sbp and dbp in the case of blood pressure) is captured in an Observation resource. When a value is missing, an Observation.dataAbsentReason is given (always ‘unknown’ (Unknown)).

Patient

See MIMIC patient. MIMIC-ED only captures subject_id and gender.

Procedure ED

One Procedure resource per row in the triage / vitalsign tables (= collection of Observations for a patient).

MIMIC-ED Table	MIMIC-ED Data Element	FHIR Data Element	FHIR Profile	Notes
triage	stay_id	Procedure.id	MimicProcedureED	Each stay_id has one triage associated with it
triage	subject_id	Procedure.subject	MimicProcedureED	Convert to UUID5
triage	stay_id	Procedure.encounter	MimicProcedureED	Convert to UUID5
triage	intime	Procedure.performedDateTime	MimicProcedureED
vitalsign	stay_id, charttime	Procedure.id	MimicProcedureED	Concat elements and convert to UUID5
vitalsign	subject_id	Procedure.subject	MimicProcedureED	Convert to UUID5
vitalsign	stay_id	Procedure.encounter	MimicProcedureED	Convert to UUID5
vitalsign	charttime	Procedure.performedDateTime	MimicProcedureED

• Procedure.status is fixed to ‘completed’ (Completed) for all MIMIC-ED procedures.
• Procedure.code is either SNOMED CT 386478007 (Triage: emergency center (procedure)) when the Procedure describes observations from the triage table, or SNOMED CT 410188000 (Taking patient vital signs assessment (procedure)) when describing observations from the vitalsign table.