BFF to PXF
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 |
| 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 |