BFF to PXF

BFF to PXF - Schemas

• Beacon v2 Models - individuals
• Phenopacket v2 schema

Information

The Phenopacket v2 schema enforces the presence of specific properties to achieve successful validation. We display in parenthesis the fields that are employed to guarantee conformity.

Version 0.31

Target model: Phenopackets v2

Entity: phenopacket

Terms

id

Source field	Target field	Notes
Generated by convert-pheno	id	Omitted in --test mode

subject

Source field	Target field	Notes
id	subject.id	Direct
info.phenopacket.vitalStatus	subject.vitalStatus	Preferred source
info.vitalStatus	subject.vitalStatus	Fallback preserved source
--default-vital-status	subject.vitalStatus.status	Used when no preserved source value is available
ALIVE	subject.vitalStatus.status	Built-in fallback when no preserved source value or CLI default is available
sex	subject.sex	Normalized to the Phenopackets enum
info.phenopacket.dateOfBirth	subject.dateOfBirth	Preferred source
info.dateOfBirth	subject.dateOfBirth	Fallback source
karyotypicSex	subject.karyotypicSex	Direct

phenotypicFeatures

Source field	Target field	Notes
phenotypicFeatures.featureType	phenotypicFeatures.type	Renamed
phenotypicFeatures.excluded	phenotypicFeatures.excluded	Direct; defaults to false when absent
phenotypicFeatures.onset	phenotypicFeatures.onset	Wrapped back into a Phenopackets time element
phenotypicFeatures.resolution	phenotypicFeatures.resolution	Wrapped back into a Phenopackets time element
phenotypicFeatures.evidence	phenotypicFeatures.evidence[]	Beacon object is emitted as a one-item array
phenotypicFeatures.evidence.info.phenopacket.evidence[]	phenotypicFeatures.evidence[]	Preferred when the original array was preserved
phenotypicFeatures.evidence.reference.notes	phenotypicFeatures.evidence.reference.description	Renamed back to the Phenopackets term

measurements

Source field	Target field	Notes
measures.assayCode	measurements.assay	Renamed
measures.measurementValue	measurements.value	Used for plain values
measures.measurementValue.typedQuantities	measurements.complexValue.typedQuantities	Used for complex values
measures.measurementValue.typedQuantities.quantityType	measurements.complexValue.typedQuantities.type	Inner key renamed
measures.observationMoment	measurements.timeObserved	Wrapped back into a Phenopackets time element
measures.date	measurements.timeObserved.timestamp	Used only when observationMoment is absent
measures.procedure	measurements.procedure	Nested procedure is remapped with the same rules

biosamples

Source field	Target field	Notes
info.phenopacket.biosamples	biosamples	Restored when present

interpretations

Source field	Target field	Notes
info.phenopacket.interpretations	interpretations	Restored when present

genes

Source field	Target field	Notes
info.phenopacket.genes	genes	Restored when present

variants

Source field	Target field	Notes
info.phenopacket.variants	variants	Restored when present

diseases

Source field	Target field	Notes
diseases.diseaseCode	diseases.term	Renamed
diseases.ageOfOnset	diseases.onset	Wrapped back into a Phenopackets time element

medicalActions

Source field	Target field	Notes
interventionsOrProcedures.procedureCode	medicalActions.procedure.code	Renamed
interventionsOrProcedures.bodySite	medicalActions.procedure.bodySite	Direct when present
interventionsOrProcedures.ageAtProcedure	medicalActions.procedure.performed	Preferred source for procedure timing
interventionsOrProcedures.dateOfProcedure	medicalActions.procedure.performed.timestamp	Used when ageAtProcedure is absent
treatments.treatmentCode	medicalActions.treatment.agent	Renamed
treatments.routeOfAdministration	medicalActions.treatment.routeOfAdministration	Direct
treatments.doseIntervals	medicalActions.treatment.doseIntervals	Direct

exposures

Source field	Target field	Notes
exposures	Not emitted	Phenopackets v2 Phenopacket does not define top-level exposures

files

Source field	Target field	Notes
info.phenopacket.files	files	Restored when present

pedigree

Source field	Target field	Notes
info.phenopacket.pedigree	pedigree	Restored when present

metaData

Source field	Target field	Notes
info.phenopacket.metaData	metaData	Preferred source
info.metaData	metaData	Fallback source
Generated by convert-pheno	metaData	Used when no preserved metadata is available and --test is not enabled