Phenopacket

A Phenopacket is an anonymous phenotypic description of an individual or biosample with potential genes of interest and/or diagnoses. It can be used for multiple use cases. For instance, it can be used to describe the phenotypic findings observed in an individual with a disease that is being studied or for an individual in whom the diagnosis is being sought. The phenopacket can contain information about genetic findings that are causative of the disease, or alternatively it can contain a reference to a VCF file if exome sequencing is being performed as a part of the differential diagnostic process. A Phenopacket can also be used to describe the constitutional phenotypic findings of an individual with cancer (a Biosample should be used to describe the phenotypic abnormalities directly associated with an extirpated or biopsied tumor).

Definition of the Phenopacket element
Field Type Multiplicity Definition
id string 1..1 arbitrary identifier. REQUIRED.
subject Individual 0..1 The proband. RECOMMENDED.
phenotypic_features List of PhenotypicFeature 0..* Phenotypic features observed in the proband. RECOMMENDED.
measurements List of Measurement 0..* Measurements performed in the proband
biosamples List of Biosample 0..* samples (e.g., biopsies), if any
interpretations List of Interpretation 0..* Interpretations related to this phenopacket
diseases List of Disease 0..* Disease(s) diagnosed in the proband
medical_actions List of MedicalAction 0..* Medical actions performed
files List of File 0..* list of files related to the subject, e.g. VCF or other high-throughput sequencing files
meta_data MetaData 1..1 Information about ontologies and references used in the phenopacket. REQUIRED.

Examples

TODO link to several longer examples.

Explanations

id

The id is an identifier specific for this phenopacket. The syntax of the identifier is application specific.

subject

This is typically the individual human (or another organism) that the Phenopacket is describing. In many cases, the individual will be a patient or proband of the study. See Individual for further information.

phenotypic_features

This is a list of phenotypic findings observed in the subject. See PhenotypicFeature for further information.

measurements

A list of measurements performed in the patient. In contrast to PhenotypicFeature, which relies on an OntologyClass to specify the observation, the Measurement can be used to report quanititative as well as ordinal or categorical measurements.

biosamples

This field describes samples that have been derived from the patient who is the object of the Phenopacket. or a collection of biosamples in isolation. See Biosample for further information.

interpretations

An optional list of Interpretation related to the phenopacket. These elements are intended to represent interpretations of disease or phenotypic findings based on genomic findings and must relate either to a genetic or genomic investigation of organismal origin (e.g., germline DNA derived from a blood sample) or from a Biosample.

diseases

This is a field for disease identifiers and can be used for listing either diagnosed or suspected conditions. The resources using these fields should define what this represents in their context. See Disease for further information.

medical_actions

A list of treatments or other medical actions performed for the person represented by this phenopacket. See MedicalAction for details.

files

This element contains a list of pointers to relevant file(s) for the subject. For example, the results of a high-throughput sequencing experiment. See File for further information.

meta_data

This element contains structured definitions of the resources and ontologies used within the phenopacket. It is expected that every valid Phenopacket contains a metaData element. See MetaData for further information.