Get all details about a person

GET

/datasets/{dataset_id}/persons/{id}

Gets a detailed view of all information available about a person

Parameters

Path Parameters

dataset_id

required

string

id

required

integer

Responses

200

Retrieved dataset information

A Phenopacket is a container for sharing an individual case or biosample with phenotypic features, diagnoses, measurements, genomic interpretations, and associated metadata.

object

id

required

A unique identifier for this phenopacket instance.

string

subject

required

The individual (patient or organism) that is the subject of this phenopacket.

object

id

required

A unique identifier for the individual within the scope of the phenopacket.

string

alternate_ids

Alternative identifiers that may be used for the individual in other systems.

Array<string>

date_of_birth

The date or age at which the individual was born.

string format: datetime

time_at_last_encounter

The age or age range of the individual when last encountered. RECOMMENDED.

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

vital_status

The vital status of the individual e.g. whether they are alive or the time and cause of death. RECOMMENDED.

object

status

required

One of UNKNOWN_STATUS, ALIVE, DECEASED. REQUIRED.

string

Allowed values: UNKNOWN_STATUS ALIVE DECEASED

time_of_death

Should be left blank if patient not known to be deceased

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

cause_of_death

Should be left blank if patient not known to be deceased

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

survival_time_in_days

Number of days the patient was alive after their primary diagnosis.

integer

sex

The phenotypic sex of the individual.

string

Allowed values: UNKNOWN_SEX MALE FEMALE OTHER_SEX

karyotypic_sex

The chromosomal (karyotypic) sex of the individual, if known.

string

Allowed values: UNKNOWN_KARYOTYPE XX XY XO XXY XXX XXYY XXXY OTHER_KARYOTYPE

gender

Self-identified gender

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

taxonomy

The taxonomic classification of the individual, typically a species identifier.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

phenotypic_features

A list of phenotypic features observed or explicitly excluded in the subject.

Array<object>

A phenotypic feature that is observed or explicitly excluded in an individual or biosample.

object

type

required

The ontology term describing the phenotypic feature.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

description

A free-text description providing additional detail about the feature.

string

excluded

Indicates whether the feature was explicitly excluded (true) or observed (false).

boolean

severity

An ontology term describing the severity of the phenotypic feature.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

modifiers

Ontology terms that modify or further specify the phenotypic feature.

Array<object>

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

onset

The time at which the phenotypic feature first became apparent.

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

resolution

The time at which the phenotypic feature resolved, if applicable.

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

evidence

Evidence supporting the assertion of this phenotypic feature.

Array<object>

Evidence supporting a phenotypic or genomic assertion.

object

evidence_code

required

An ontology term describing the type of evidence.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

reference

Representation of the source of the evidence

object

id

required

Identifier of the external reference.

string

description

Description of the reference.

string

measurements

Quantitative or qualitative measurements obtained from the subject.

Array<object>

A quantitative or qualitative measurement obtained from an individual or biosample.

object

description

Free text

string

assay

required

The assay or test used to generate the measurement.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

value

required

One of:

object

The measured value, either quantitative or categorical.

object

quantity

required

A numeric value with an associated unit.

object

value

required

The numeric value of the quantity.

number

unit

required

The unit in which the value is expressed.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

object

The measured value, either quantitative or categorical.

object

ontology_class

required

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

time_observed

The time at which the measurement was observed or recorded.

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

procedure

The procedure associated with obtaining the measurement.

object

code

required

Clinical procedure performed. REQUIRED.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

body_site

Specific body site where the procedure was performed

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

performed

Age/time when the procedure was performed

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

biosamples

Biosamples collected from the subject, such as tissue samples or cell lines.

Array<object>

A biological sample derived from an individual, such as tissue, blood, or cells.

object

id

required

A unique identifier for the biosample.

string

individual_id

The identifier of the individual from whom the biosample was derived.

string

derived_from_id

Id of the biosample from which the current biosample was derived (if applicable)

string

description

A free-text description of the biosample.

string

sampled_tissue

The tissue or anatomical site from which the biosample was obtained.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

sample_type

Type of material, e.g., RNA, DNA, Cultured cells.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

phenotypic_features

Phenotypic features observed or excluded in the context of this biosample.

Array<object>

A phenotypic feature that is observed or explicitly excluded in an individual or biosample.

object

type

required

The ontology term describing the phenotypic feature.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

description

A free-text description providing additional detail about the feature.

string

excluded

Indicates whether the feature was explicitly excluded (true) or observed (false).

boolean

severity

An ontology term describing the severity of the phenotypic feature.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

modifiers

Ontology terms that modify or further specify the phenotypic feature.

Array<object>

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

onset

The time at which the phenotypic feature first became apparent.

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

resolution

The time at which the phenotypic feature resolved, if applicable.

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

evidence

Evidence supporting the assertion of this phenotypic feature.

Array<object>

Evidence supporting a phenotypic or genomic assertion.

object

evidence_code

required

An ontology term describing the type of evidence.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

reference

Representation of the source of the evidence

object

id

required

Identifier of the external reference.

string

description

Description of the reference.

string

measurements

Measurements obtained from this biosample.

Array<object>

A quantitative or qualitative measurement obtained from an individual or biosample.

object

description

Free text

string

assay

required

The assay or test used to generate the measurement.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

value

required

One of:

object

The measured value, either quantitative or categorical.

object

quantity

required

A numeric value with an associated unit.

object

value

required

The numeric value of the quantity.

number

unit

required

The unit in which the value is expressed.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

object

The measured value, either quantitative or categorical.

object

ontology_class

required

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

time_observed

The time at which the measurement was observed or recorded.

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

procedure

The procedure associated with obtaining the measurement.

object

code

required

Clinical procedure performed. REQUIRED.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

body_site

Specific body site where the procedure was performed

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

performed

Age/time when the procedure was performed

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

taxonomy

Species of the sampled individual

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

time_of_collection

The time at which the biosample was collected.

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

histological_diagnosis

Disease diagnosis that was inferred from the histological examination. RECOMMENDED.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

tumor_progression

Indicates primary, metastatic, recurrent. RECOMMENDED.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

tumor_grade

Term representing the tumor grade

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

pathological_stage

The pathological stage associated with the biosample, if applicable.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

pathological_tnm_finding

TNM pathological findings associated with the biosample.

Array<object>

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

diagnostic_markers

Clinically relevant biomarkers. RECOMMENDED.

Array<object>

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

procedure

The procedure used to extract the biosample. RECOMMENDED.

object

code

required

Clinical procedure performed. REQUIRED.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

body_site

Specific body site where the procedure was performed

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

performed

Age/time when the procedure was performed

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

files

List of files related to the biosample, e.g. VCF or other high-throughput sequencing files

Array<object>

A reference to an external file associated with the phenopacket.

object

uri

required

A URI pointing to the file location.

string format: uri

individual_to_file_identifiers

The mapping between the Individual.id or Biosample.id to any identifier in the file. RECOMMENDED.

string

file_attributes

A map of attributes pertaining to the file or its contents.

object

material_sample

Status of specimen (tumor tissue, normal control, etc.). RECOMMENDED.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

sample_processing

How the specimen was processed

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

sample_storage

How the specimen was stored

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

interpretations

Clinical or research interpretations derived from phenotypic and/or genomic data.

Array<object>

A clinical or research interpretation derived from phenotypic and/or genomic data.

object

id

required

A unique identifier for the interpretation.

string

progress_status

required

The overall status of the interpretation.

string

Allowed values: UNKNOWN_PROGRESS IN_PROGRESS COMPLETED SOLVED UNSOLVED

diagnosis

The diagnosis resulting from this interpretation, if any.

object

disease

required

The disease or condition diagnosed, represented as an ontology term.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

genomic_interpretations

The genomic elements assessed as being responsible for the disease or empty

Array<object>

An interpretation of genomic data, such as a variant or gene-level assessment.

object

subject_or_biosample_id

required

The identifier of the subject or biosample to which this interpretation applies.

string

interpretation_status

required

The status of this genomic interpretation.

string

Allowed values: UNKNOWN_STATUS REJECTED CANDIDATE CONTRIBUTORY CAUSATIVE

call

required

One of:

object

Represents an identifier for a gene, using the Gene Descriptor from the VRSATILE Framework

object

value_id

required

Official identifier of the gene. REQUIRED.

string

symbol

required

Official gene symbol. REQUIRED.

string

description

A free-text description of the gene

string

alternate_ids

Alternative identifier(s) of the gene

Array<string>

xrefs

Related concept IDs (e.g. gene ortholog IDs) may be placed in xrefs

Array<string>

alternate_symbols

Alternative symbol(s) of the gene

Array<string>

object

A clinical or research interpretation of a specific genomic variant.

object

acmg_pathogenicity_classification

required

One of the five ACMG pathogenicity categories, or NOT_PROVIDED. The default is NOT_PROVIDED

string

Allowed values: NOT_PROVIDED BENIGN LIKELY_BENIGN UNCERTAIN_SIGNIFICANCE LIKELY_PATHOGENIC PATHOGENIC

therapeutic_actionability

required

The therapeutic actionability of the variant, default is UNKNOWN_ACTIONABILITY

string

Allowed values: UNKNOWN_ACTIONABILITY NOT_ACTIONABLE ACTIONABLE

variation_descriptor

required

A genetic/genomic variant

object

id

required

A unique identifier for this VariationDescriptor instance.

string

variation

One of:

object

A contiguous change at a specific sequence location.

object

id

Globally unique VRS identifier.

string

location

required

Location of the allele on a reference sequence.

object

sequence_id

required

CURIE or URI identifying the reference sequence.

string

interval

required

Continuous interval on a sequence.

object

start

required

0-based inclusive start position.

integer

end

required

0-based exclusive end position.

integer

state

required

Resulting sequence state.

object

sequence

required

Alternate sequence.

string

object

A set of alleles known to co-occur on the same molecule.

object

id

string

members

required

Array<object>

A contiguous change at a specific sequence location.

object

id

Globally unique VRS identifier.

string

location

required

Location of the allele on a reference sequence.

object

sequence_id

required

CURIE or URI identifying the reference sequence.

string

interval

required

Continuous interval on a sequence.

object

start

required

0-based inclusive start position.

integer

end

required

0-based exclusive end position.

integer

state

required

Resulting sequence state.

object

sequence

required

Alternate sequence.

string

object

Copy number variation over a genomic region.

object

id

string

location

required

A location on a biological sequence.

object

sequence_id

required

CURIE or URI identifying the reference sequence.

string

interval

required

Continuous interval on a sequence.

object

start

required

0-based inclusive start position.

integer

end

required

0-based exclusive end position.

integer

copies

required

Absolute number of copies.

integer

object

Unstructured textual representation of a variation.

object

id

string

value

required

string

label

A primary human-readable label for the variation.

string

alternate_labels

Additional human-readable labels or synonyms for the variation.

Array<string>

description

A free-text description of the variation.

string

gene_context

The gene context in which this variation is interpreted.

object

value_id

required

Official identifier of the gene. REQUIRED.

string

symbol

required

Official gene symbol. REQUIRED.

string

description

A free-text description of the gene

string

alternate_ids

Alternative identifier(s) of the gene

Array<string>

xrefs

Related concept IDs (e.g. gene ortholog IDs) may be placed in xrefs

Array<string>

alternate_symbols

Alternative symbol(s) of the gene

Array<string>

expressions

Expressions of the variation using standardized syntaxes such as HGVS or SPDI.

Array<object>

A syntactic expression of a variation.

object

syntax

required

Expression syntax (e.g. hgvs.c, hgvs.g, spdi).

string

value

required

Expression string.

string

vcf_record

A VCF-based representation of the variation.

object

genome_assembly

required

Reference genome assembly (e.g. GRCh38).

string

chrom

required

Chromosome identifier.

string

pos

required

1-based genomic position.

integer

ref

required

Reference allele.

string

alt

required

Alternate allele.

string

vrs_ref_allele_seq

The reference allele sequence used for VRS Allele normalization. This must exactly match the reference sequence at the VRS location.

string

allelic_state

The allelic state of the variation (e.g. heterozygous, homozygous).

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

structural_type

The structural classification of the variant.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

molecule_context

required

The molecular context in which the variation is described.

string

Allowed values: genomic transcript protein

external_references

External database references supporting or describing this variation.

Array<object>

Reference to an external resource.

object

id

required

Identifier of the external reference.

string

description

Description of the reference.

string

extensions

A list of extensions for additional information not captured by the core schema.

Array<object>

An extension element providing additional structured information using ontology terms or custom fields.

object

name

required

A CURIE or URI identifying the meaning of the extension.

string

NCIT:C171003

value

required

The value of the extension.

string

summary

Additional data about this interpretation

string

diseases

Diseases or conditions diagnosed or considered for the subject.

Array<object>

A disease or condition that is diagnosed, suspected, or explicitly excluded.

object

term

required

The disease or condition term.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

excluded

Indicates whether the disease was explicitly excluded.

boolean

onset

The time or age of disease onset, if known.

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

resolution

An element representing the age of resolution (abatement) of the disease

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

disease_stage

List of terms representing the disease stage e.g. AJCC stage group.

Array<object>

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

clinical_tnm_finding

List of terms representing the tumor TNM score

Array<object>

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

primary_site

The primary site of disease

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

laterality

The primary site of disease

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

medical_actions

Medical actions performed

Array<object>

One of:

object

This element describes medications, procedures, other actions taken for clinical management. The element is a list of options.

object

procedure

required

Represents a clinical procedure performed on a subject. For example a surgical or diagnostic procedure such as a biopsy.

object

code

required

Clinical procedure performed. REQUIRED.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

body_site

Specific body site where the procedure was performed

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

performed

Age/time when the procedure was performed

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

treatment_target

The condition or disease that this treatment was intended to address

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

treatment_intent

Whether the intention of the treatment was curative, palliative…

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

response_to_treatment

How the patient responded to the treatment

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

adverse_events

Any adverse effects experienced by the patient attributed to the treatment

Array<object>

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

treatment_termination_reason

The reason that the treatment was stopped.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

object

This element describes medications, procedures, other actions taken for clinical management. The element is a list of options.

object

treatment

required

This represents treatment with an agent such as a drug (pharmaceutical agent), broadly defined as prescription and over-the-counter medicines, vaccines, and large-molecule biologic therapies.

object

agent

required

The drug or therapeutic agent. REQUIRED.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

route_of_administration

How was the drug administered. RECOMMENDED.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

dose_intervals

Dosages. RECOMMENDED.

object

quantity

required

Amount administered in one dose. REQUIRED.

object

value

required

The numeric value of the quantity.

number

unit

required

The unit in which the value is expressed.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

schedule_frequency

required

How often doses are administered per day (or other indicated duration). REQUIRED.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

interval

required

The specific interval over which the dosage was administered in the indicated quantity. REQUIRED.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

drug_type

Context of the drug administration

string

Allowed values: UNKNOWN_DRUG_TYPE PRESCRIPTION EHR_MEDICATION_LIST ADMINISTRATION_RELATED_TO_PROCEDURE

cumulative_dose

The cumulative dose administered during the period of the treatment.

object

value

required

The numeric value of the quantity.

number

unit

required

The unit in which the value is expressed.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

treatment_target

The condition or disease that this treatment was intended to address

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

treatment_intent

Whether the intention of the treatment was curative, palliative…

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

response_to_treatment

How the patient responded to the treatment

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

adverse_events

Any adverse effects experienced by the patient attributed to the treatment

Array<object>

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

treatment_termination_reason

The reason that the treatment was stopped.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

object

This element describes medications, procedures, other actions taken for clinical management. The element is a list of options.

object

radiation_therapy

required

Radiation therapy (or radiotherapy) uses ionizing radiation, generally as part of cancer treatment to control or kill malignant cells.

object

modality

required

The modality of radiation therapy (e.g., electron, photon,…). REQUIRED.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

body_site

required

The anatomical site where radiation therapy was administered. REQUIRED.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

dosage

required

The total dose given in units of Gray (Gy). REQUIRED.

integer

fractions

required

The total number of fractions delivered as part of treatment. REQUIRED.

integer

treatment_target

The condition or disease that this treatment was intended to address

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

treatment_intent

Whether the intention of the treatment was curative, palliative…

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

response_to_treatment

How the patient responded to the treatment

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

adverse_events

Any adverse effects experienced by the patient attributed to the treatment

Array<object>

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

treatment_termination_reason

The reason that the treatment was stopped.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

object

This element describes medications, procedures, other actions taken for clinical management. The element is a list of options.

object

therapeutic_regimen

required

This element represents a therapeutic regimen which will involve a specified set of treatments for a particular condition.

object

identifier

required

One of:

object

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

object

Reference to an external resource.

object

id

required

Identifier of the external reference.

string

description

Description of the reference.

string

start_time

When the regimen was started. RECOMMENDED.

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

end_time

When the regimen ended. An empty end_time with a populated start_time would indicate the regimen was ongoing. RECOMMENDED.

object

>= 1 properties <= 1 properties

gestational_age

Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery.

object

weeks

required

Completed weeks of gestation according to the above definition. REQUIRED.

integer

days

Number of completed days of gestation in addition to the provided weeks. RECOMMENDED, If available.

integer

<= 6

age

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

age_range

The AgeRange element is intended to be used when the age of a subject is represented by a bin, e.g., 5-10 years. Bins such as this are used in some situations in order to protect the privacy of study participants, whose age is then represented by bins such as 45-49 years, 50-54 years, 55-59 years, and so on.

object

start

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

end

required

An age represented as an ISO 8601 duration.

object

iso8601duration

required

The age encoded as an ISO 8601 duration string (e.g. P5Y).

string

ontology_class

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

timestamp

string format: date-time

interval

A time interval with optional start and end timestamps.

object

start

required

The start time of the interval.

string format: date-time

end

required

The end time of the interval.

string format: date-time

regimen_status

required

Current status of the regimen for the enclosing MedicalAction on the Individual. REQUIRED.

string

Allowed values: UNKNOWN_STATUS STARTED COMPLETED DISCONTINUED

treatment_target

The condition or disease that this treatment was intended to address

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

treatment_intent

Whether the intention of the treatment was curative, palliative…

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

response_to_treatment

How the patient responded to the treatment

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

adverse_events

Any adverse effects experienced by the patient attributed to the treatment

Array<object>

A reference to a term in a controlled ontology.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

treatment_termination_reason

The reason that the treatment was stopped.

object

id

required

The compact identifier (CURIE or IRI) for the ontology term.

string

label

required

A human-readable label for the ontology term.

string

files

External files associated with this phenopacket, such as genomic data files.

Array<object>

A reference to an external file associated with the phenopacket.

object

uri

required

A URI pointing to the file location.

string format: uri

individual_to_file_identifiers

The mapping between the Individual.id or Biosample.id to any identifier in the file. RECOMMENDED.

string

file_attributes

A map of attributes pertaining to the file or its contents.

object

metaData

Metadata describing the provenance, resources, and updates for this phenopacket.

object

created

required

The timestamp at which the phenopacket was created.

string format: date-time

created_by

required

The agent or organization that created the phenopacket.

string

submitted_by

Name of person who submitted the phenopacket

string

resources

Ontology and data resources referenced in the phenopacket.

Array<object>

Describes an ontology or data resource used in the phenopacket.

object

id

required

A unique identifier for the resource.

string

name

required

Formal name of the resource or ontology e.g. human phenotype ontology.

string

namespace_prefix

required

Namespace prefix of the resource e.g HP. REQUIRED.

string

url

required

A URL pointing to the resource homepage or documentation.

string

version

required

The version of the resource used.

string

iri_prefix

required

Internationalized Resource Identifier such as http://purl.obolibrary.org/obo/HP_. REQUIRED.

string

updates

A history of updates made to the phenopacket.

Array<object>

A record describing a modification made to the phenopacket.

object

timestamp

required

The time at which the update occurred.

string format: date-time

updated_by

Information about the person/organisation/network that has updated the phenopacket.

string

comment

Textual comment about the changes made to the content and/or reason for the update.

string

phenopacket_schema_version

required

Schema version of the current phenopacket

string

external_references

A list of ExternalReference (such as the PubMed id of a publication from which a phenopacket was derived).

Array<object>

Reference to an external resource.

object

id

required

Identifier of the external reference.

string

description

Description of the reference.

string

400

The request was not processed, as the request parameters did not adhere to the specification

object

query

Error object container

object

error

required

Name/type of the error that occurred

string

ServerError

message

required

Message explaining why the error occurred

string

An unspecified server error occurred

query

object

error

InvalidInput

message

FOO is not an acceptable field

401

The request was not processed, as the request was missing an authentication token

object

query

Error object container

object

error

required

Name/type of the error that occurred

string

ServerError

message

required

Message explaining why the error occurred

string

An unspecified server error occurred

query

object

error

InvalidInput

message

FOO is not an acceptable field

403

The request was not processed, as the user in the given authentication token does not have sufficient privileges to proceed

object

query

Error object container

object

error

required

Name/type of the error that occurred

string

ServerError

message

required

Message explaining why the error occurred

string

An unspecified server error occurred

query

object

error

InvalidInput

message

FOO is not an acceptable field

404

The request was not processed, as the requested object was not found

object

query

Error object container

object

error

required

Name/type of the error that occurred

string

ServerError

message

required

Message explaining why the error occurred

string

An unspecified server error occurred

query

object

error

NotFound

message

The requested resource could not be located

default

Unspecified server error encountered

object

query

Error object container

object

error

required

Name/type of the error that occurred

string

ServerError

message

required

Message explaining why the error occurred

string

An unspecified server error occurred