PXF 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.

Version 0.25¶

Terms¶

diseases¶

PXF JSON path	BFF JSON path
diseases	diseases
diseases.term	diseases.diseaseCode
diseases.onset	diseases.ageOfOnset

ethnicity¶

NA

exposures¶

PXF JSON path	BFF JSON path
exposures	exposures
exposures.type	exposures.exposureCode
exposures.occurrence.timestamp	exposures.date

geographicOrigin¶

NA

id¶

PXF JSON path	BFF JSON path
subject.id	id

info¶

PXF JSON path	BFF JSON path
dateOfBirth, genes, metaData, variants, interpretations, files, biosample	info

interventionsOrProcedures¶

PXF JSON path	BFF JSON path
medicalActions.procedure	interventionsOrProcedures
medicalActions.procedure.code	interventionsOrProcedures.procedureCode
medicalActions.procedure.performed	interventionsOrProcedures.ageAtProcedure

karyotypicSex¶

PXF JSON path	BFF JSON path
subject.karyotypicSex	karyotypicSex

measures¶

PXF JSON path	BFF JSON path
measurements	measures
measurements.assay	measures.assayCode
measurements.value	measures.measurementValue
measurements.complexValue.typedQuantities.type	measures.measurementValue.typedQuantities.quantityType
measurements.timeObserved	measures.observationMoment
measurements.procedure	measures.procedure

pedigrees¶

NA

phenotypicFeatures¶

PXF JSON path	BFF JSON path
phenotypicFeatures	phenotypicFeatures
phenotypicFeatures.type	phenotypicFeatures.featureType
phenotypicFeatures.negated	phenotypicFeatures.excluded
phenotypicFeatures.evidence (array)	phenotypicFeatures.evidence (v2.0.0 is still object)

sex¶

PXF JSON path	BFF JSON path
subject.sex	sex

treatments¶

PXF JSON path	BFF JSON path
medicalActions.treatment	treatments
medicalActions.treatment.agent	treatments.treatmentCode