OMOP to BFF - Schemas

Information

The Beacon v2 schema enforces the presence of specific properties to achieve successful validation. In cases where no suitable match is found, DEFAULT values are employed to guarantee conformity.

Terms¶

diseases¶

OMOP Table(s)	OMOP Variable	BFF JSON path
CONDITION_OCCURRENCE, PERSON	condition_start_date, birth_datetime	diseases.ageOfOnset.iso8601duration
CONDITION_OCCURRENCE	condition_concept_id	diseases.diseaseCode
CONDITION_OCCURRENCE	All variables	diseases._info
CONDITION_OCCURRENCE	condition_status_concept_id	diseases.stage
CONDITION_OCCURRENCE	person_id, visit_occurrence_id	diseases._visit

ethnicity¶

OMOP Table(s)	OMOP Variable	BFF JSON path
PERSON	race_source_value	ethnicity

exposures¶

OMOP Table(s)	OMOP Variable	BFF JSON path
OBSERVATION, PERSON	observation_date, birth_datetime	exposures.ageAtExposure.iso8601duration
OBSERVATION	observation_date	exposures.date
	DEFAULT	exposures.duration
OBSERVATION	All variables	exposures._info
OBSERVATION	observation_concept_id	exposures.exposureCode
OBSERVATION	unit_concept_id	exposures.unit
OBSERVATION	value_as_number	exposures.value

geographicOrigin¶

OMOP Table(s)	OMOP Variable	BFF JSON path
PERSON	ethnicity_source_value	geographicOrigin

id¶

OMOP Table(s)	OMOP Variable	BFF JSON path
PERSON	person_id	id

info¶

OMOP Table(s)	OMOP Variable	BFF JSON path
PERSON	All variables	info.PERSON
PERSON	birth_datetime	info.dateOfBirth

interventionsOrProcedures¶

OMOP Table(s)	OMOP Variable	BFF JSON path
PROCEDURE_OCCURRENCE, PERSON	procedure_date, birth_datetime	interventionsOrProcedures.ageAtProcedure.iso8601duration
PROCEDURE_OCCURRENCE	procedure_date	interventionsOrProcedures.dateOfProcedure
PROCEDURE_OCCURRENCE	All variables	interventionsOrProcedures._info
PROCEDURE_OCCURRENCE	procedure_concept_id	interventionsOrProcedures.procedureCode

karyotypicSex¶

NA

measures¶

OMOP Table(s)	OMOP Variable	BFF JSON path
MEASUREMENT	measurement_concept_id	measures.assayCode
MEASUREMENT	measurement_date	measures.date
MEASUREMENT	measurement_concept_id	measures.assayCode
MEASUREMENT	unit_concept_id	measures.measurementValue.quantity.unit
MEASUREMENT	value_as_number	measures.measurementValue.quantity.value
MEASUREMENT	operator_concept_id, value_as_number, unit_concept_id	measures.measurementValue.quantity.referenceRange
MEASUREMENT	All variables	measures._info
MEASUREMENT, PERSON	measurement_date, birth_datetime	measures.observationMoment.age.iso8601duration
MEASUREMENT		measures.procedure (= measures.assayCode)
MEASUREMENT	person_id, visit_occurrence_id	diseases._visit

pedigrees¶

NA

phenotypicFeatures¶

OMOP Table(s)	OMOP Variable	BFF JSON path
OBSERVATION	observation_concept_id	phenotypicFeatures.featureType
OBSERVATION	All variables	phenotypicFeatures._info
OBSERVATION, PERSON	observation_date, birth_datetime	phenotypicFeatures.onset.isoduration
OBSERVATION	person_id, visit_occurrence_id	phenotypicFeatures._visit

sex¶

OMOP Table(s)	OMOP Variable	BFF JSON path
PERSON	gender_concept_id	sex

treatments¶

OMOP Table(s)	OMOP Variable	BFF JSON path
DRUG_EXPOSURE, PERSON	drug_exposure_start_date, birth_datetime	treatments.ageOfOnset.age.iso8601duration
	DEFAULT	treatments.date
DRUG_EXPOSURE	All variables	treatments._info
	DEFAULT	treatments.doseIntervals
	DEFAULT	treatments.routeOfAdministration
DRUG_EXPOSURE	drug_concept_id	treatments.treatmentCode
DRUG_EXPOSURE	person_id, visit_occurrence_id	treatments._visit

About exposures

exposures terms are obtained from this CSV file. You can use a different csv file with the option --exposures-file.