Closed mbaudis closed 2 years ago
Are the Treatment
differences still correct? These look to be the same now e.g. they both use an array of DoseInterval
.
@julesjacobsen Yes, the notes here were the initial comparison. While I've added some changes after adjustments we'll document the relation to Phenopackets in the documentation (https://github.com/ga4gh-beacon/beacon-v2-unity-testing/blob/main/docs/formats-standards.md or page linked from there). (@mrueda @laurenfromont)
The comparison has been added to the documentation: http://docs.genomebeacons.org/formats-standards/#phenopackets.
We'll update there and through individual issues/PRs.
In the current data models, many schemas are either directly compatible to Phenopackets v2 building blocks or at least reflect them in spirit. The following lists elements with notes regarding their Phenopackets compatibility.
While the Beacon v2 default model's schemas do not per se have to reflect PXF schemas, we target an as-close-as-possible alignment to promote/leverage GA4GH-wide standardization.
This issue here serves for a general review regarding current and possible future alignment, with individual changes being processed in separate PRs/issues.
Top-level differences
The Phenopackets model is centered around the
Phenopacket
, which is the collector and integrator of all sub-schemas (with the addition of the externalFamily
andCohort
schemas). WhilePhenopacket
usually describes information related to asubject
- which is defined in anIndividual
- and the top level elements inPhenopacket
relate to a specificproband
(measurements
as "Measurements performed in the proband"), the phenopacket itself does not explicitely represent an individual.In contrast, the Beacon v2 default model uses a hierarchy in which biosamples reference individuals directly (if existing). For most purposes one can equate Beacon's
Individual
with a merge of Phenopacket's corePhenopacket
andIndividual
parameters.Beacon v2
==
PXF v2Age
AgeRange
Evidence
KaryotypicSex
ReferenceRange
While
unit
in Beacon points to aUnit
definition, this is itself anOntologyTerm
i.e. structurally the same.Value
Beacon v2
=~
PXF v2 (e.g. renamed or additional parameters)ComplexValue
Renamed
ComplexValue.TypedQuantity.quantityType
compared to GA4GH Phenopackets v2ComplexValue.TypedQuantity.type
due to problematic use oftype
as parameterExternalReference
Renamed
ExternalReference.notes
compared to GA4GH Phenopackets v2ExternalReference.description
due to problematic use ofdescription
as parameterMeasurement
Added
notes
anddate
.PhenotypicFeature
featureType
type
severityLevel
(re-used definition reflecting an ontology term)severity
(ontology class)notes
Procedure
procedureCode
code
ageAtProcedure
(TimeElement)performed
(TimeElement
)dateOfProcedure
(ISO date)TimeElement
The specific parameters have been aligned w/ some differences in naming or use of general parameters.
ageGroup
ontology_class
age
age
(Age
)ageRange
age_range
(AgeRange
)gestationalAge
gestational_age
(GestationalAge
)timestamp
(TimeStamp
)interval
(TimeInterval
)Treatment
Beacon still has an
ageOfOnset
parameter (?).Beacon v2
~
PXF v2 (e.g. multiple/complex differences)Disease
Pedigree
While the Beacon & Phenopackets schemas for "pedigree" representation are not aligned, they may become superseded by the GA4GH pedigree standard currenty under development.
Sex
Beacon directly uses the (IMO preferable) representation through an ontology term, while PXF uses an ordinal mapping
2022-03-17: Updated for last adjustments (KaryotypicSex, Treatment ...)
2022-01-18: Updated w/ "Top-level differences"