MIMIC Implementation Guide - Local Development build (v1.3.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Mimic Fhir Mappings

MIMIC to FHIR Mappings

The MIMIC-IV database was converted into FHIR. The tables from MIMIC-IV 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. In the following sections you will see tables detailing the mapping from each MIMIC table to these MIMIC-FHIR profiles.

Condition

MIMIC-IV Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
diagnosis_icd	hadm_id, seq_num, icd_code	Condition.id	MimicCondition	Id made up of concatenation of hadm_id, seq_num, and icd_code, converted to UUID5
diagnosis_icd	subject_id	Condition.subject	MimicCondition
diagnosis_icd	hadm_id	Condition.encounter	MimicCondition
d_icd_diagnoses	icd_code	Condition.code.coding.code	MimicCondition
d_icd_diagnoses	long_title	Condition.code.coding.display	MimicCondition

• Condition.category set to fixed value of ‘encounter-diagnosis’

Encounter

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
admissions	hadm_id	Encounter.id	MimicEncounter	Hadm_id converted to UUID5
admissions	hadm_id	Encounter.identifier.value	MimicEncounter
admissions	admission_type	Encounter.class	MimicEncounter
admissions	admission_type	Encounter.priority	MimicEncounter
admissions	admission_location	Encounter.hospitalization.admitSource	MimicEncounter
admissions	discharge_location	Encounter.hospitalization.dischargeDisposition	MimicEncounter
admissions	subject_id	Encounter.subject	MimicEncounter
admissions	admittime	Encounter.period.start	MimicEncounter
admissions	dischtime	Encounter.period.end	MimicEncounter
admissions	dischtime	Encounter.period.end	MimicEncounter
hcpcsevents	hcpcs_cd	Encounter.type.coding.code	MimicEncounter
hcpcsevents	short_description	Encounter.type.coding.display	MimicEncounter
services	curr_service	Encounter.serviceType	MimicEncounter
transfers	careunit	Encounter.location.reference	MimicEncounter
transfers	intime	Encounter.location.period.start	MimicEncounter
transfers	outtime	Encounter.location.period.end	MimicEncounter

• Encounter.status is fixed to ‘finished’ for all MIMIC encounters
• Encounter.serviceProvider is set to an UUID for BIDMC organization

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
icustays	stay_id	Encounter.id	MimicEncounter	Stay_id converted to UUID5
icustays	stay_id	Encounter.identifier.value	MimicEncounter
icustays	first_careunit	Encounter.location.reference	MimicEncounter
icustays	intime	Encounter.period.start	MimicEncounter
icustays	outtime	Encounter.period.end	MimicEncounter
icustays	subject_id	Encounter.subject	MimicEncounter	Convert to UUID
icustays	hadm_id	Encounter.partOf	MimicEncounter	Links to MIMIC_Encounter’s
transfers	intime	Encounter.location.period.start	MimicEncounter	Take the min intime in the transfers table
transfers	outtime	Encounter.location.period.end	MimicEncounter	Take the max outtime in the transfers table

• Encounter.status is fixed to ‘finished’ for all MIMIC encounters
• Encounter.class is fixed to ‘ACUTE’
• Encounter.type is fixed to SCT code 308335008 for “Patient encounter procedure”

MedicationAdministration

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
emar	subject_id	MedicationAdministration.subject	MimicMedicationAdministration	convert to UUID5
emar	hadm_id	MedicationAdministration.context	MimicMedicationAdministration	convert to UUID5
emar	charttime	MedicationAdminstration.effectiveDateTime	MimicMedicationAdministration
emar_detail	emar_id, parent_field_ordinal	MedicationAdministration.id	MimicMedicationAdministration	Id is concatenation of mimic data elements and converted to UUID5
emar_detail	pharmacy_id	MedicationAdministration.request	MimicMedicationAdministration
emar_detail	dose_given, dose_given_unit	MedicationAdministration.dosage.text	[MedicationAdministration]	concat the text and units
emar_detail	site	MedicationAdministration.site	[MedicationAdministration]
emar_detail	route	MedicationAdministration.route	[MedicationAdministration]
emar_detail	event_txt	MedicationAdministration.route	[MedicationAdministration]
emar_detail	infusion_rate	MedicationAdministration.rateQuantity.value	[MedicationAdministration]
emar_detail	infusion_rate_unit	MedicationAdministration.rateQuantity.unit	[MedicationAdministration]	also set for code element
emar_detail	product_code	MedicationAdministration.medicationCodeableConcept	MimicMedicationAdministration	product code used if present
emar	medication	MedicationAdministration.medicationCodeableConcept	MimicMedicationAdministration	medication used if product code not present
poe	order_type	MedicationAdministration.medicationCodeableConcept	MimicMedicationAdministration	Used for IV and TPN medication

• MedicationAdministration.status is fixed to ‘completed’
• MedicationAdministration.medicationCodeableConcept set to ‘UNK’ if product_code, medication, and poe.order_type are all NULL

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
inputevents	stay_id, orderid, itemid	MedicationAdministration.id	MimicMedicationAdministrationICU	Id is concatenation of mimic data elements and converted to UUID5
inputevents	subject_id	MedicationAdministration.subject	MimicMedicationAdministrationICU	convert to UUID5
inputevents	stay_id	MedicationAdministration.context	MimicMedicationAdministrationICU	convert to UUID5
inputevents	starttime	MedicationAdministration.effectivePeriod.start	MimicMedicationAdministrationICU
inputevents	rate	MedicationAdministration.effectiveDateTime	MimicMedicationAdministrationICU
inputevents	endtime	MedicationAdministration.effectivePeriod.end	MimicMedicationAdministrationICU	only set period if inputevents.rate is null
inputevents	ordercategorydescription	MedicationAdministration.dosage.method	MimicMedicationAdministrationICU
inputevents	amount	MedicationAdministration.dosage.dose.value	MimicMedicationAdministrationICU
inputevents	amountuom	MedicationAdministration.dosage.dose.unit	MimicMedicationAdministrationICU	used for dose.unit and dose.code
inputevents	rate	MedicationAdministration.dosage.rateQuantity.value	MimicMedicationAdministrationICU
inputevents	rateuom	MedicationAdministration.dosage.rateQuantity.unit	MimicMedicationAdministrationICU	ised for rateQuantity unit and code
d_items	itemid	MedicationAdministration.medicationCodeableConcept.coding.code	MimicMedicationAdministrationICU
d_items	label	MedicationAdministration.medicationCodeableConcept.coding.display	MimicMedicationAdministrationICU

• MedicationAdministration.status is fixed to ‘completed’

MedicationDispense

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
pharmacy	pharmacy_id	MedicationDispense.id	MimicMedicationDispense	convert to UUID5
pharmacy	pharmacy_id	MedicationDispense.identifier	MimicMedicationDispense
pharmacy	medication	MedicationDispense.medicationCodeableConcept	MimicMedicationDispense
pharmacy	subject	MedicationDispense.subject_id	MimicMedicationDispense	convert to UUID5
pharmacy	hadm_id	MedicationDispense.context	MimicMedicationDispense	convert to UUID5
pharmacy	pharmacy_id	MedicationDispense.authorizingPrescription	MimicMedicationDispense	convert to UUID5
pharmacy	fill_quantity	MedicationDispense.quantity	MimicMedicationDispense
pharmacy	route	MedicationDispense.dosageInstruction.route	MimicMedicationDispense
pharmacy	frequency	MedicationDispense.dosageInstruction.timing.code	MimicMedicationDispense
pharmacy	duration	MedicationDispense.dosageInstruction.timing.duration	MimicMedicationDispense
pharmacy	one_hr_max	MedicationDispense.dosageInstruction.maxDosePerPeriod	MimicMedicationDispense

• MedicationDispense.status is fixed to ‘completed’

MedicationRequest

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
prescriptions	pharmacy_id	MedicationRequest.id	MimicMedicationRequest	convert to UUID5
prescriptions	pharmacy_id	MedicationRequest.identifier	MimicMedicationRequest
prescriptions	subject_id	MedicationRequest.subject	MimicMedicationRequest	convert to UUID5
prescriptions	hadm_id	MedicationRequest.encounter	MimicMedicationRequest	convert to UUID5
prescriptions	drug_code	MedicationRequest.medicationReference	MimicMedicationRequest	convert to UUID5
prescriptions	status	MedicationRequest.status	MimicMedicationRequest
prescriptions	entertime	MedicationRequest.authoredOn	MimicMedicationRequest
prescriptions	prod_strength	MedicationRequest.dosageInstruction.text	MimicMedicationRequest
prescriptions	route	MedicationRequest.dosageInstruction.route	MimicMedicationRequest
prescriptions	dose_val_rx	MedicationRequest.dosageInstruction.doseAndRate.doseQuantity.value	MimicMedicationRequest
prescriptions	dose_unit_rx	MedicationRequest.dosageInstruction.doseAndRate.doseQuantity.unit	MimicMedicationRequest
prescriptions	frequency	MedicationRequest.dosageInstruction.timing.code	MimicMedicationRequest
prescriptions	duration	MedicationRequest.dosageInstruction.timing.repeat.duration	MimicMedicationRequest
prescriptions	one_hr_max	MedicationRequest.dosageInstruction.maxDosePerPeriod	MimicMedicationRequest
prescriptions	starttime	MedicationRequest.dispenseRequest.validityPeriod.start	MimicMedicationRequest
prescriptions	stoptime	MedicationRequest.dispenseRequest.validityPeriod.end	MimicMedicationRequest

• MedicationRequest.intent is fixed to ‘order’

Observation - labevents

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
labevents	labevent_id	Observation.id	MimicObservationLabevents	Convert to UUID5
labevents	labevent_id	Observation.identifier	MimicObservationLabevents
labevents	status	Observation.status	MimicObservationLabevents
labevents	subject_id	Observation.subject	MimicObservationLabevents	Convert to UUID5
labevents	hadm_id	Observation.encounter	MimicObservationLabevents	Convert to UUID5
labevents	specimen_id	Observation.specimen	MimicObservationLabevents	Convert to UUID5
labevents	charttime	Observation.effectiveDateTime	MimicObservationLabevents
labevents	storetime	Observation.issued	MimicObservationLabevents
labevents	valuenum	Observation.valueQuantity.value	MimicObservationLabevents
labevents	valueuom	Observation.valueQuantity.unit	MimicObservationLabevents	Used for valueQuantity unit and code
labevents	value	Observation.valueString	MimicObservationLabevents	Only used if MIMIC-IV valuenum is NULL
labevents	comments	Observation.valueString	MimicObservationLabevents	Only used if MIMIC-IV valuenum is NULL and value is NULL
labevents	comments	Observation.note.text	MimicObservationLabevents	Always capture the comment, but does not always match valueString
labevents	flag	Observation.interpretation	MimicObservationLabevents
labevents	ref_range_lower	Observation.referenceRange.low.value	MimicObservationLabevents
labevents	valueuom	Observation.referenceRange.low.unit	MimicObservationLabevents	Used for unit and code
labevents	ref_range_upper	Observation.referenceRange.high.value	MimicObservationLabevents
labevents	valueuom	Observation.referenceRange.high.unit	MimicObservationLabevents	Used for unit and code
labevents	priority	Observation.extension:lab-priority	MimicObservationLabevents	Set value to a custom extension LabPriority
d_labitems	itemid	Observation.code.coding.code	MimicObservationLabevents
d_labitems	label	Observation.code.coding.display	MimicObservationLabevents

• Observation.category is set to code ‘laboratory’
• Observation.value[x] has a 0..1 cardinality, hence only one measurement is captured in an Observation resource. When a value is missing, an Observation.dataAbsentReason is given (always ‘unknown’ (Unknown)).

Observation - microbiology

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
microbiologyevents	micro_specimen_id, test_itemid	Observation.id	MimicObservationMicroTest	Concat elements and convert to UUID5
microbiologyevents	subject_id	Observation.subject	MimicObservationMicroTest	Convert to UUID5
microbiologyevents	hadm_id	Observation.encounter	MimicObservationMicroTest	Convert to UUID5
microbiologyevents	micro_specimen_id	Observation.specimen	MimicObservationMicroTest	Convert to UUID5
microbiologyevents	test_itemid	Observation.code.coding.code	MimicObservationMicroTest
microbiologyevents	test_name	Observation.code.coding.display	MimicObservationMicroTest
microbiologyevents	charttime	Observation.effectiveDateTime	MimicObservationMicroTest
microbiologyevents	org_itemid	Observation.hasMember	MimicObservationMicroTest	Group all the references to org_itemid associated with the test_itemid
microbiologyevents	org_itemid	Observation.valueString	MimicObservationMicroTest

• Observation.status is fixed to ‘final’
• Observation.category is set to code ‘laboratory’
• Observation.value[x] has a 0..1 cardinality, hence only one measurement is captured in an Observation resource. When a value is missing, an Observation.dataAbsentReason is given (always ‘unknown’ (Unknown)).

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
microbiologyevents	micro_specimen_id, test_itemid, org_itemid	Observation.id	MimicObservationMicroOrg	Concat elements and convert to UUID5
microbiologyevents	subject_id	Observation.subject	MimicObservationMicroOrg	Convert to UUID5
microbiologyevents	hadm_id	Observation.encounter	MimicObservationMicroOrg	Convert to UUID5
microbiologyevents	org_itemid	Observation.code.coding.code	MimicObservationMicroOrg
microbiologyevents	org_name	Observation.code.coding.display	MimicObservationMicroOrg
microbiologyevents	charttime	Observation.effectiveDateTime	MimicObservationMicroOrg
microbiologyevents	micro_specimen_id, test_itemid	Observation.derivedFrom	MimicObservationMicroOrg	Point to the parent microbiology test
microbiologyevents	microevent_id	Observation.hasMember	MimicObservationMicroOrg	Group all the references to microevent_id associated with an org_itemid and test_itemid
microbiologyevents	org_itemid	Observation.valueString	MimicObservationMicroOrg

• Observation.status is fixed to ‘final’
• Observation.category is set to code ‘laboratory’
• Observation.value[x] has a 0..1 cardinality, hence only one measurement is captured in an Observation resource. When a value is missing, an Observation.dataAbsentReason is given (always ‘unknown’ (Unknown)).

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
microbiologyevents	microevent_id	Observation.id	MimicObservationMicroSusc	Convert to UUID5
microbiologyevents	microevent_id	Observation.identifer	MimicObservationMicroSusc
microbiologyevents	subject_id	Observation.subject	MimicObservationMicroSusc	Convert to UUID5
microbiologyevents	hadm_id	Observation.encounter	MimicObservationMicroSusc	Convert to UUID5
microbiologyevents	ab_itemid	Observation.code.coding.code	MimicObservationMicroSusc
microbiologyevents	ab_name	Observation.code.coding.display	MimicObservationMicroSusc
microbiologyevents	storetime	Observation.effectiveDateTime	MimicObservationMicroSusc
microbiologyevents	comments	Observation.note.text	MimicObservationMicroSusc
microbiologyevents	dilution_value	Observation.extension:dilution_details	MimicObservationMicroSusc	Set dilution value to custom extension dilution_details
microbiologyevents	micro_specimen_id, test_itemid, org_itemid	Observation.derivedFrom	MimicObservationMicroSusc	Reference back to parent Observation. Concat elements and convert to UUID5

• Observation.status is fixed to ‘final’
• Observation.category is set to code ‘laboratory’
• Observation.value[x] has a 0..1 cardinality, hence only one measurement is captured in an Observation resource. When a value is missing, an Observation.dataAbsentReason is given (always ‘unknown’ (Unknown)).

Observation - ICU

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
chartevents	stay_id, itemid, value	Observation.id	MimicObservationChartevents	Concat MIMIC elements and convert to UUID5
chartevents	subject_id	Observation.subject	MimicObservationChartevents	Convert to UUID5
chartevents	stay_id	Observation.encounter	MimicObservationChartevents	Convert to UUID5
chartevents	charttime	Observation.effectiveDateTime	MimicObservationChartevents
chartevents	storetime	Observation.issued	MimicObservationChartevents
chartevents	valuenum	Observation.valueQuantity.value	MimicObservationChartevents
chartevents	valueuom	Observation.valueQuantity.unit	MimicObservationChartevents	Used for both unit and code element
chartevents	value	Observation.valueString	MimicObservationChartevents	Only store valueString if valueQuantity is not present
chartevents	lownormalvalue	Observation.referenceRange.low.value	MimicObservationChartevents
chartevents	valueuom	Observation.referenceRange.low.unit	MimicObservationChartevents	Used for both unit and code element
chartevents	highnormalvalue	Observation.referenceRange.high.value	MimicObservationChartevents
chartevents	valueuom	Observation.referenceRange.high.unit	MimicObservationChartevents	Used for both unit and code element
d_items	category	Observation.category	MimicObservationChartevents
d_items	itemid	Observation.code.coding.code	MimicObservationChartevents
d_items	label	Observation.code.coding.display	MimicObservationChartevents

• Observation.status is fixed to ‘final’

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
datetimeevents	stay_id, charttime, itemid	Observation.id	MimicObservationDatetimeevents	Concat MIMIC elements and convert to UUID5
datetimeevents	subject_id	Observation.subject	MimicObservationDatetimeevents	Convert to UUID5
datetimeevents	stay_id	Observation.encounter	MimicObservationDatetimeevents	Convert to UUID5
datetimeevents	charttime	Observation.effectiveDateTime	MimicObservationDatetimeevents
datetimeevents	storetime	Observation.issued	MimicObservationDatetimeevents
datetimeevents	value	Observation.valueDateTime	MimicObservationDatetimeevents
d_items	category	Observation.category	MimicObservationDatetimeevents
d_items	itemid	Observation.code.coding.code	MimicObservationDatetimeevents
d_items	label	Observation.code.coding.display	MimicObservationDatetimeevents

• Observation.status is fixed to ‘final’

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
outputevents	stay_id, charttime, itemid	Observation.id	MimicObservationOutputevents	Concat MIMIC elements and convert to UUID5
outputevents	subject_id	Observation.subject	MimicObservationOutputevents	Convert to UUID5
outputevents	stay_id	Observation.encounter	MimicObservationOutputevents	Convert to UUID5
outputevents	charttime	Observation.effectiveDateTime	MimicObservationOutputevents
outputevents	storetime	Observation.issued	MimicObservationOutputevents
outputevents	value	Observation.valueQuantity.value	MimicObservationOutputevents
outputevents	valueuom	Observation.valueQuantity.unit	MimicObservationOutputevents	Used for unit and code elements
d_items	category	Observation.category	MimicObservationOutputevents
d_items	itemid	Observation.code.coding.code	MimicObservationOutputevents
d_items	label	Observation.code.coding.display	MimicObservationOutputevents

• Observation.status is fixed to ‘final’

Location

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
transfers	careunit	Location.id	MimicLocation	careunit converted to UUID5
transfers	careunit	Location.name	MimicLocation

• Location.physicalType set to a fixed code ‘wa’ for Wards
• Location.status is set to ‘active’
• Location.managingOrganization set to BIDMC

Patient

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
patients	subject_id	Patient.id	MimicPatient	Convert to UUID5
patients	subject_id	Patient.identifier	MimicPatient
patients	gender	Patient.gender	MimicPatient
patients	anchor_age	Patient.birthDate	MimicPatient	Using transfers.intime as a relative point to create a birthDate
patients	dod	Patient.deceasedDateTime	MimicPatient
patients	gender	Patient.extension:birthsex	MimicPatient
admissions	ethnicity	Patient.extension:race	MimicPatient	Map MIMIC ethnicity to the FHIR race categories
admissions	ethnicity	Patient.extension:ethnicity	MimicPatient	Map MIMIC ethnicity to the FHIR ethnicity groups
admissions	marital_status	Patient.maritalStatus	MimicPatient
admissions	language	Patient.communication.language	MimicPatient

• Patient.name is created with a combination of “Patient_” and subject_id being concatenated
• Patient.managingOrganization is set to BIDMC

Procedure

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
procedures_icd	hadm_id, seq_num, icd_code	Procedure.id	MimicProcedure	Concat elements and convert to UUID5
procedures_icd	subject_id	Procedure.subject	MimicProcedure	Convert to UUID5
procedures_icd	hadm_id	Procedure.encounter	MimicProcedure	Convert to UUID5
procedures_icd	chartdate	Procedure.performedDateTime	MimicProcedure
procedures_icd	icd_code	Procedure.code.coding.code	MimicProcedure
procedures_icd	icd_version	Procedure.code.coding.system	MimicProcedure	ICD Version used to select FHIR ICD codesystem
d_icd_procedures	long_title	Procedure.code.coding.display	MimicProcedure

• Procedure.status is fixed to ‘completed’ (Completed) for all procedures.

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
procedureevents	stay_id, order_id, itemid	Procedure.id	MimicProcedureICU	Concat elements and convert to UUID5
procedureevents	subject_id	Procedure.subject	MimicProcedureICU	Convert to UUID5
procedureevents	stay_id	Procedure.encounter	MimicProcedureICU	Convert to UUID5
procedureevents	starttime	Procedure.performedPeriod.start	MimicProcedureICU
procedureevents	endtime	Procedure.performedPeriod.end	MimicProcedureICU
procedureevents	location	Procedure.bodySite	MimicProcedureICU
procedureevents	statusdescription	Procedure.status	MimicProcedureICU
procedureevents	ordercategoryname	Procedure.category	MimicProcedureICU
procedureevents	itemid	Procedure.code.coding.code	MimicProcedureICU
d_items	label	Procedure.code.coding.display	MimicProcedureICU

Specimen

MimicSpecimen is mapped from both MIMIC-IV tables labevents and microbiologyevents.

MIMIC Table	MIMIC Data Element	FHIR Data Element	FHIR Profile	Notes
	labevents	specimen_id	Specimen.id	MimicSpecimen	Convert to UUID5
	labevents	specimen_id	Specimen.identifier	MimicSpecimen
	labevents	subject_id	Specimen.subject	MimicSpecimen	Convert to UUID5
	labevents	charttime	Specimen.collection.collectedDateTime	MimicSpecimen
	labevents	fluid	Specimen.type.coding.code	MimicSpecimen
	microbiologyevents	micro_specimen_id	Specimen.id	MimicSpecimen	Convert to UUID5
	microbiologyevents	micro_specimen_id	Specimen.identifier	MimicSpecimen
	microbiologyevents	subject_id	Specimen.subject	MimicSpecimen	Convert to UUID5
	microbiologyevents	charttime	Specimen.collection.collectedDateTime	MimicSpecimen
	microbiologyevents	spec_itemid	Specimen.type.coding.code	MimicSpecimen
	microbiologyevents	spec_type_desc	Specimen.type.coding.code	MimicSpecimen