Skip to content

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