A Phenopacket is an anonymous phenotypic description of an individual or biosample with potential genetic findings and/or diagnoses of interest. 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 genome scale 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 rstbiosample should be used to describe the phenotypic abnormalities directly associated with an extirpated or biopsied tumor).
Definition of thePhenopacketelement
Field Type Multiplicity Definition id string 1..1 arbitrary identifier. REQUIRED. subject rstindividual0..1 The proband. RECOMMENDED. phenotypic_features List of phenotypicfeature0..* Phenotypic features observed in the proband. RECOMMENDED. measurements List of rstmeasurement0..* Measurements performed in the proband biosamples List of rstbiosample0..* samples (e.g., biopsies), if any interpretations List of rstinterpretation0..* Interpretations related to this phenopacket diseases List of rstdisease0..* Disease(s) diagnosed in the proband medical_actions List of rstmedicalaction0..* Medical actions performed files List of rstfile0..* list of files related to the subject, e.g. VCF or other high-throughput sequencing files meta_data rstmetadata1..1 Information about ontologies and references used in the phenopacket. REQUIRED.
TODO link to several longer examples.
The id is an identifier specific for this phenopacket. The syntax of the identifier is application specific.
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 rstindividual for further information.
This is a list of phenotypic findings observed in the subject. See phenotypicfeature for further information.
A list of measurements performed in the patient. In contrast to phenotypicfeature, which relies on an rstontologyclass to specify the observation, the rstmeasurement can be used to report quanititative as well as ordinal or categorical measurements.
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 rstbiosample for further information.
An optional list of rstinterpretation 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 rstbiosample.
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 rstdisease for further information.
A list of treatments or other medical actions performed for the person represented by this phenopacket. See rstmedicalaction for details.
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 rstfile 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 rstmetadata for further information.