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.
Version 0.25
Terms
diseases
OMOP Table(s)
OMOP Variable
BFF JSON path
CONDITION_OCCURRENCE, PERSON
condition_start_date, birth_datetime
diseases.ageOfOnset
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
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
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
value_as_concept_id
measures.measurementValue
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
MEASUREMENT
measurement_date, birth_datetime
measures.procedure.ageAtProcedure
MEASUREMENT
measurement_date
measures.procedure.dateOfProcedure
MEASUREMENT
measurement_type_concept_id
measures.procedure.prodecureCode
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
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
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
.
last change 2023-06-09 by Manuel Rueda