ppsc.v202 package

A package with types corresponding to the v2.0.2 release of the Phenopacket Schema.

class ppsc.v202.Phenopacket(id: str, meta_data: MetaData, subject: Individual | None = None, phenotypic_features: Iterable[PhenotypicFeature] | None = None, measurements: Iterable[Measurement] | None = None, biosamples: Iterable[Biosample] | None = None, interpretations: Iterable[Interpretation] | None = None, diseases: Iterable[Disease] | None = None, medical_actions: Iterable[MedicalAction] | None = None, files: Iterable[File] | None = None)

Bases: MessageMixin

property id: str

property subject: Individual | None

property phenotypic_features: MutableSequence[PhenotypicFeature]

property measurements: MutableSequence[Measurement]

property biosamples: MutableSequence[Biosample]

property interpretations: MutableSequence[Interpretation]

property diseases: MutableSequence[Disease]

property medical_actions: MutableSequence[MedicalAction]

property files: MutableSequence[File]

property meta_data: MetaData

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Individual(id: str, alternate_ids: Iterable[str] | None = None, date_of_birth: Timestamp | None = None, time_at_last_encounter: TimeElement | None = None, vital_status: VitalStatus | None = None, sex: Sex | None = None, karyotypic_sex: KaryotypicSex | None = None, gender: OntologyClass | None = None, taxonomy: OntologyClass | None = None)

Bases: MessageMixin

property id: str | None

property alternate_ids: MutableSequence[str]

property date_of_birth: Timestamp | None

property time_at_last_encounter: TimeElement | None

property vital_status: VitalStatus | None

property sex: Sex | None

property karyotypic_sex: KaryotypicSex | None

property gender: OntologyClass | None

property taxonomy: OntologyClass | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.VitalStatus(status: Status, time_of_death: TimeElement | None = None, cause_of_death: OntologyClass | None = None, survival_time_in_days: int | None = None)

Bases: MessageMixin

TODO: add docs.

class Status(value)

Bases: Enum

TODO: add docs.

UNKNOWN_STATUS = 0

ALIVE = 1

DECEASED = 2

property status: Status

property time_of_death: TimeElement | None

property cause_of_death: OntologyClass | None

property survival_time_in_days: int | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Sex(value)

Bases: Enum

An enumeration used to represent the sex of an individual. This element does not represent gender identity or KaryotypicSex, but instead represents typical “phenotypic sex”, as would be determined by a midwife or physician at birth.

UNKNOWN_SEX = 0

Not assessed or not available. Maps to NCIT:C17998

FEMALE = 1

Female sex. Maps to NCIT:C46113.

MALE = 2

Male sex. Maps to NCIT:C46112

OTHER_SEX = 3

It is not possible to accurately assess the applicability of MALE/FEMALE. Maps to NCIT:C45908

class ppsc.v202.KaryotypicSex(value)

Bases: Enum

An enumeration.

UNKNOWN_KARYOTYPE = 0

XX = 1

XY = 2

XO = 3

XXY = 4

XXX = 5

XXYY = 6

XXXY = 7

XXXX = 8

XYY = 9

OTHER_KARYOTYPE = 10

class ppsc.v202.GeneDescriptor(value_id: str, symbol: str, description: str | None = None, alternate_ids: Iterable[str] | None = None, xrefs: Iterable[str] | None = None, alternate_symbols: Iterable[str] | None = None)

Bases: MessageMixin

property value_id: str

property symbol: str

property description: str

property alternate_ids: MutableSequence[str]

property xrefs: MutableSequence[str]

property alternate_symbols: MutableSequence[str]

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.AcmgPathogenicityClassification(value)

Bases: Enum

An enumeration.

NOT_PROVIDED = 0

BENIGN = 1

LIKELY_BENIGN = 2

UNCERTAIN_SIGNIFICANCE = 3

LIKELY_PATHOGENIC = 4

PATHOGENIC = 5

class ppsc.v202.TherapeuticActionability(value)

Bases: Enum

An enumeration.

UNKNOWN_ACTIONABILITY = 0

NOT_ACTIONABLE = 1

ACTIONABLE = 2

class ppsc.v202.VariantInterpretation(acmg_pathogenicity_classification: AcmgPathogenicityClassification, therapeutic_actionability: TherapeuticActionability, variation_descriptor: VariationDescriptor)

Bases: MessageMixin

property acmg_pathogenicity_classification: AcmgPathogenicityClassification

property therapeutic_actionability: TherapeuticActionability

property variation_descriptor: VariationDescriptor

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.GenomicInterpretation(subject_or_biosample_id: str, interpretation_status: InterpretationStatus, call: GeneDescriptor | VariantInterpretation)

Bases: MessageMixin

class InterpretationStatus(value)

Bases: Enum

An enumeration.

UNKNOWN_STATUS = 0

REJECTED = 1

CANDIDATE = 2

CONTRIBUTORY = 3

CAUSATIVE = 4

property subject_or_biosample_id: str

property interpretation_status: InterpretationStatus

property call: GeneDescriptor | VariantInterpretation

property gene_descriptor: GeneDescriptor | None

property variant_interpretation: VariantInterpretation | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Diagnosis(disease: OntologyClass, genomic_interpretations: Iterable[GenomicInterpretation] | None = None)

Bases: MessageMixin

property disease: OntologyClass

property genomic_interpretations: MutableSequence[GenomicInterpretation]

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Interpretation(id: str, progress_status: ProgressStatus, diagnosis: Diagnosis | None = None, summary: str | None = None)

Bases: MessageMixin

class ProgressStatus(value)

Bases: Enum

An enumeration.

UNKNOWN_PROGRESS = 0

IN_PROGRESS = 1

COMPLETED = 2

SOLVED = 3

UNSOLVED = 4

property id: str

property progress_status: ProgressStatus

property diagnosis: Diagnosis | None

property summary: str | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.ReferenceRange(unit: OntologyClass, low: float, high: float)

Bases: MessageMixin

property unit: OntologyClass

property low: float

property high: float

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Quantity(unit: OntologyClass, value: float, reference_range: ReferenceRange | None = None)

Bases: MessageMixin

property unit: OntologyClass

property value: float

property reference_range: ReferenceRange | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

to_message() → Message

Get a protobuf representation of the class.

class ppsc.v202.TypedQuantity(type: OntologyClass, quantity: Quantity)

Bases: MessageMixin

property type: OntologyClass

property quantity: Quantity

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.ComplexValue(typed_quantities: Iterable[TypedQuantity])

Bases: MessageMixin

property typed_quantities: MutableSequence[TypedQuantity]

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

to_message() → Message

Get a protobuf representation of the class.

class ppsc.v202.Value(value: Quantity | OntologyClass)

Bases: MessageMixin

property value: Quantity | OntologyClass

property quantity: Quantity | None

property ontology_class: OntologyClass | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Measurement(assay: OntologyClass, measurement_value: Value | ComplexValue, description: str | None = None, time_observed: TimeElement | None = None, procedure: Procedure | None = None)

Bases: MessageMixin

property assay: OntologyClass

property measurement_value: Value | ComplexValue

property value: Value | None

property complex_value: ComplexValue | None

property description: str | None

property time_observed: TimeElement | None

property procedure: Procedure | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.TherapeuticRegimen(identifier: ExternalReference | OntologyClass, regimen_status: RegimenStatus, start_time: TimeElement | None = None, end_time: TimeElement | None = None)

Bases: MessageMixin

class RegimenStatus(value)

Bases: Enum

An enumeration.

UNKNOWN_STATUS = 0

STARTED = 1

COMPLETED = 2

DISCONTINUED = 3

property identifier: ExternalReference | OntologyClass

property external_reference: ExternalReference | None

property ontology_class: OntologyClass | None

property regimen_status: RegimenStatus

property start_time: TimeElement | None

property end_time: TimeElement | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.RadiationTherapy(modality: OntologyClass, body_site: OntologyClass, dosage: int, fractions: int)

Bases: MessageMixin

property modality: OntologyClass

property body_site: OntologyClass

property dosage: int

property fractions: int

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.DrugType(value)

Bases: Enum

An enumeration.

UNKNOWN_DRUG_TYPE = 0

PRESCRIPTION = 1

EHR_MEDICATION_LIST = 2

ADMINISTRATION_RELATED_TO_PROCEDURE = 3

class ppsc.v202.DoseInterval(quantity: Quantity, schedule_frequency: OntologyClass, interval: TimeInterval)

Bases: MessageMixin

property quantity: Quantity

property schedule_frequency: OntologyClass

property interval: TimeInterval

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Treatment(agent: OntologyClass, route_of_administration: OntologyClass | None = None, dose_intervals: Iterable[DoseInterval] | None = None, drug_type: DrugType | None = None, cumulative_dose: Quantity | None = None)

Bases: MessageMixin

property agent: OntologyClass

property route_of_administration: OntologyClass | None

property dose_intervals: MutableSequence[DoseInterval]

property drug_type: DrugType | None

property cumulative_dose: Quantity | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

to_message() → Message

Get a protobuf representation of the class.

class ppsc.v202.MedicalAction(action: Procedure | Treatment | RadiationTherapy | TherapeuticRegimen, treatment_target: OntologyClass | None = None, treatment_intent: OntologyClass | None = None, response_to_treatment: OntologyClass | None = None, adverse_events: Iterable[OntologyClass] | None = None, treatment_termination_reason: OntologyClass | None = None)

Bases: MessageMixin

property action: Procedure | Treatment | RadiationTherapy | TherapeuticRegimen

property procedure: Procedure

property treatment: Treatment

property radiation_therapy: RadiationTherapy

property therapeutic_regimen: TherapeuticRegimen

property treatment_target: OntologyClass | None

property treatment_intent: OntologyClass | None

property response_to_treatment: OntologyClass | None

property adverse_events: MutableSequence[OntologyClass]

property treatment_termination_reason: OntologyClass | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Expression(syntax: str, value: str, version: str | None = None)

Bases: MessageMixin

property syntax: str

property value: str

property version: str | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Extension(name: str, value: str)

Bases: MessageMixin

property name: str

property value: str

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.VcfRecord(genome_assembly: str, chrom: str, pos: int, ref: str, alt: str, id: str | None = None, qual: str | None = None, filter: str | None = None, info: str | None = None)

Bases: MessageMixin

property genome_assembly: str

property chrom: str

property pos: int

property ref: str

property alt: str

property id: str | None

property qual: str | None

property filter: str | None

property info: str | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.MoleculeContext(value)

Bases: Enum

An enumeration.

unspecified_molecule_context = 0

genomic = 1

transcript = 2

protein = 3

class ppsc.v202.VariationDescriptor(id: str, molecule_context: MoleculeContext, label: str | None = None, description: str | None = None, gene_context: GeneDescriptor | None = None, expressions: Iterable[Expression] | None = None, vcf_record: VcfRecord | None = None, xrefs: Iterable[str] | None = None, alternate_labels: Iterable[str] | None = None, extensions: Iterable[Extension] | None = None, structural_type: OntologyClass | None = None, vrs_ref_allele_seq: str | None = None, allelic_state: OntologyClass | None = None)

Bases: MessageMixin

property id: str

property molecule_context: MoleculeContext

property label: str | None

property description: str | None

property gene_context: GeneDescriptor | None

property expressions: MutableSequence[Expression]

property vcf_record: VcfRecord | None

property xrefs: MutableSequence[str]

property alternate_labels: MutableSequence[str]

property extensions: MutableSequence[Extension]

property structural_type: OntologyClass | None

property vrs_ref_allele_seq: str | None

property allelic_state: OntologyClass | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.PhenotypicFeature(type: OntologyClass, excluded: bool = False, description: str | None = None, severity: OntologyClass | None = None, modifiers: Iterable[OntologyClass] | None = None, onset: TimeElement | None = None, resolution: TimeElement | None = None, evidence: Iterable[Evidence] | None = None)

Bases: MessageMixin

property type: OntologyClass

property excluded: bool

property description: str | None

property severity: OntologyClass | None

property modifiers: MutableSequence[OntologyClass]

property onset: TimeElement | None

property resolution: TimeElement | None

property evidence: MutableSequence[Evidence]

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Disease(term: OntologyClass, excluded: bool = False, onset: TimeElement | None = None, resolution: TimeElement | None = None, disease_stage: Iterable[OntologyClass] | None = None, clinical_tnm_finding: Iterable[OntologyClass] | None = None, primary_site: OntologyClass | None = None, laterality: OntologyClass | None = None)

Bases: MessageMixin

property term: OntologyClass

property excluded: bool

property onset: TimeElement | None

property resolution: TimeElement | None

property disease_stage: MutableSequence[OntologyClass]

property clinical_tnm_finding: MutableSequence[OntologyClass]

property primary_site: OntologyClass | None

property laterality: OntologyClass | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Biosample(id: str, individual_id: str | None = None, derived_from_id: str | None = None, description: str | None = None, sampled_tissue: OntologyClass | None = None, sample_type: OntologyClass | None = None, phenotypic_features: Iterable[PhenotypicFeature] | None = None, measurements: Iterable[Measurement] | None = None, taxonomy: OntologyClass | None = None, time_of_collection: TimeElement | None = None, histological_diagnosis: OntologyClass | None = None, tumor_progression: OntologyClass | None = None, tumor_grade: OntologyClass | None = None, pathological_stage: OntologyClass | None = None, pathological_tnm_finding: Iterable[OntologyClass] | None = None, diagnostic_markers: Iterable[OntologyClass] | None = None, procedure: Procedure | None = None, files: Iterable[File] | None = None, material_sample: OntologyClass | None = None, sample_processing: OntologyClass | None = None, sample_storage: OntologyClass | None = None)

Bases: MessageMixin

property id: str

property individual_id: str | None

property derived_from_id: str | None

property description: str | None

property sampled_tissue: OntologyClass | None

property sample_type: OntologyClass | None

property phenotypic_features: MutableSequence[PhenotypicFeature]

property measurements: MutableSequence[Measurement]

property taxonomy: OntologyClass | None

property time_of_collection: TimeElement | None

property histological_diagnosis: OntologyClass | None

property tumor_progression: OntologyClass | None

property tumor_grade: OntologyClass | None

property pathological_stage: OntologyClass | None

property pathological_tnm_finding: MutableSequence[OntologyClass]

property diagnostic_markers: MutableSequence[OntologyClass]

property procedure: Procedure | None

property files: MutableSequence[File]

property material_sample: OntologyClass | None

property sample_processing: OntologyClass | None

property sample_storage: OntologyClass | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.MetaData(created: Timestamp, created_by: str, submitted_by: str | None = None, resources: Iterable[Resource] | None = None, updates: Iterable[Update] | None = None, phenopacket_schema_version: str = '2.0.2', external_references: Iterable[ExternalReference] | None = None)

Bases: MessageMixin

property created: Timestamp

property created_by: str

property submitted_by: str | None

property resources: MutableSequence[Resource]

property updates: MutableSequence[Update]

property phenopacket_schema_version: str

property external_references: MutableSequence[ExternalReference]

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Resource(id: str, name: str, url: str, version: str, namespace_prefix: str, iri_prefix: str)

Bases: MessageMixin

property id: str

property name: str

property url: str

property version: str

property namespace_prefix: str

property iri_prefix: str

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

to_message() → Message

Get a protobuf representation of the class.

class ppsc.v202.Update(timestamp: Timestamp, updated_by: str | None = None, comment: str | None = None)

Bases: MessageMixin

property timestamp: Timestamp

property updated_by: str

property comment: str

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

to_message() → Message

Get a protobuf representation of the class.

class ppsc.v202.OntologyClass(id: str, label: str)

Bases: MessageMixin

OntologyClass represents classes (terms) from ontologies, and is used in many places throughout the Phenopacket standard. It is a simple, two element message that represents the identifier and the label of an ontology class.

>>> from ppsc.v202 import OntologyClass

>>> oc = OntologyClass(id='HP:0001250', label='Seizure')
>>> oc.id
'HP:0001250'
>>> oc.label
'Seizure'

Parameters:

• id – a str with a CURIE-style identifier (e.g. HP:0001250).

• label – a str with a human-readable class name (e.g. Seizure).

property id: str

Get a str with the ontology class identifier.

property label: str

Get a str with the human-readable class name.

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.ExternalReference(id: str | None = None, reference: str | None = None, description: str | None = None)

Bases: MessageMixin

property id: str

property reference: str

property description: str

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Evidence(evidence_code: OntologyClass, reference: ExternalReference | None = None)

Bases: MessageMixin

property evidence_code: OntologyClass

property reference: ExternalReference | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Procedure(code: OntologyClass, body_site: OntologyClass | None = None, performed: TimeElement | None = None)

Bases: MessageMixin

property code: OntologyClass

property body_site: OntologyClass | None

property performed: TimeElement | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.GestationalAge(weeks: int, days: int | None = None)

Bases: MessageMixin

property weeks: int

property days: int | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Age(iso8601duration: str)

Bases: MessageMixin

property iso8601duration: str

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.AgeRange(start: Age, end: Age)

Bases: MessageMixin

property start

property end: Age

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.TimeInterval(start: Timestamp, end: Timestamp)

Bases: MessageMixin

property start: Timestamp

property end: Timestamp

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.TimeElement(element: GestationalAge | Age | AgeRange | OntologyClass | Timestamp | TimeInterval)

Bases: MessageMixin

TODO: better description

property element: GestationalAge | Age | AgeRange | OntologyClass | Timestamp | TimeInterval

property age: Age | None

property age_range: AgeRange | None

property ontology_class: OntologyClass

property timestamp: Timestamp

property interval: TimeInterval

property gestational_age: GestationalAge | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Timestamp(seconds: int, nanos: int)

Bases: ToProtobuf, FromProtobuf

This Timestamp implementation is functionally equivalent to protobuf’s timestamp.

Per protobuf API documentation, A Timestamp represents a point in time independent of any time zone or local calendar, encoded as a count of seconds and fractions of seconds at nanosecond resolution. The count is relative to an epoch at UTC midnight on January 1, 1970, in the proleptic Gregorian calendar which extends the Gregorian calendar backwards to year one.

Consult the Phenopacket Schema documentation for more information.

Examples

Here we show how to create a Timestamp from various inputs.

>>> from ppsc import Timestamp

Let’s create a timestamp from a date time string:

>>> ts = Timestamp.from_str('1970-01-01T00:00:30Z')
>>> ts.seconds, ts.nanos
(30, 0)

Note, we indicate that the timestamp is in UTC by adding Z suffix.

We can also create a timestamp from a local time. Let’s create the same Timestamp but now in Eastern Daylight Time (EDT) which is 4 hours behind UTC:

>>> ts_local = Timestamp.from_str('1969-12-31T20:00:30-04:00')
>>> ts_local == ts
True

We can also create timestamp from a datetime object:

>>> from datetime import datetime, date, time, timezone
>>> d = date(1970, 1, 1)
>>> t = time(0, 0, 30)
>>> dt = datetime.combine(d, t, tzinfo=timezone.utc)
>>> ts_dt = Timestamp.from_datetime(dt)
>>> ts_dt == ts
True

Last, we can create timestamp directly from seconds and nanoseconds:

>>> ts_raw = Timestamp(30, 0)
>>> ts_raw == ts
True

and we can convert the timestamp to a UTC date time string:

>>> ts_raw.as_str()
'1970-01-01T00:00:30Z'

property seconds: int

property nanos: int

as_datetime() → datetime

Convert timestamp into Python’s datetime object.

The datetime is always in UTC.

Example

>>> from ppsc import Timestamp
>>> ts = Timestamp(10, 500)
>>> dt = ts.as_datetime()

Now we can access the datetime components:

>>> dt.year, dt.month, dt.day, dt.hour, dt.minute, dt.second
(1970, 1, 1, 0, 0, 10)

including the time zone:

>>> dt.tzname()
'UTC'

as_str(fmt: str = '%Y-%m-%dT%H:%M:%SZ') → str

Convert timestamp into a date time string.

Example

>>> from ppsc import Timestamp
>>> ts = Timestamp(0, 500_000)
>>> ts.as_str()
'1970-01-01T00:00:00Z'

We can use different formatting:

>>> ts.as_str('%Y-%m-%dT%H:%M:%S.%f%Z')
'1970-01-01T00:00:00.000500UTC'

static from_str(val: str, fmt: str = '%Y-%m-%dT%H:%M:%S%z')

Create Timestamp from a date time string.

Parameters:

• val – the date time str.

• fmt – the date time format string.

static from_datetime(dt: datetime)

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.File(uri: str, individual_to_file_identifiers: Mapping[str, str] | None = None, file_attributes: Mapping[str, str] | None = None)

Bases: MessageMixin

property uri: str

property individual_to_file_identifiers: MutableMapping[str, str]

property file_attributes: MutableMapping[str, str]

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Gene(gene_id: str)

Bases: MessageMixin

property gene_id: str

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Text(definition: str)

Bases: MessageMixin

property definition: str

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Number(value: int | str)

Bases: MessageMixin

property value: int

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.IndefiniteRange(value: int, comparator: str)

Bases: MessageMixin

property value: int

property comparator: str

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

to_message() → Message

Get a protobuf representation of the class.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.DefiniteRange(min: int, max: int)

Bases: MessageMixin

property min: int

property max: int

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

to_message() → Message

Get a protobuf representation of the class.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.SimpleInterval(start: int, end: int)

Bases: MessageMixin

property start: int

property end: int

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

to_message() → Message

Get a protobuf representation of the class.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.SequenceInterval(start: Number | IndefiniteRange | DefiniteRange, end: Number | IndefiniteRange | DefiniteRange)

Bases: MessageMixin

SequenceInterval is a complicated case which is

property start: Number | IndefiniteRange | DefiniteRange

property start_number: Number | None

property start_indefinite_range: IndefiniteRange | None

property start_definite_range: DefiniteRange | None

property end: Number | IndefiniteRange | DefiniteRange

property end_number: Number | None

property end_indefinite_range: IndefiniteRange | None

property end_definite_range: DefiniteRange | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

to_dict(out: MutableMapping[str, Any])

Write itself into a dictionary composed of primitive or Python compound types.

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.SequenceLocation(sequence_id: str, interval: SequenceInterval | SimpleInterval)

Bases: MessageMixin

property sequence_id: str

property interval: SequenceInterval | SimpleInterval

property sequence_interval

property simple_interval

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.SequenceState(sequence: str)

Bases: MessageMixin

property sequence: str

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.LiteralSequenceExpression(sequence: str)

Bases: MessageMixin

property sequence: str

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.DerivedSequenceExpression(location: SequenceLocation, reverse_complement: bool = False)

Bases: MessageMixin

property location: SequenceLocation

property reverse_complement: bool

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.RepeatedSequenceExpression(seq_expr: LiteralSequenceExpression | DerivedSequenceExpression, count: Number | IndefiniteRange | DefiniteRange)

Bases: MessageMixin

property seq_expr: LiteralSequenceExpression | DerivedSequenceExpression

property literal_sequence_expression: LiteralSequenceExpression | None

property derived_sequence_expression: DerivedSequenceExpression | None

property count: Number | IndefiniteRange | DefiniteRange

property number: Number | None

property indefinite_range: IndefiniteRange | None

property definite_range

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.CytobandInterval(start: str, end: str)

Bases: MessageMixin

property start: str

property end: str

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

to_message() → Message

Get a protobuf representation of the class.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.ChromosomeLocation(species_id: str, chr: str, interval: CytobandInterval)

Bases: MessageMixin

property species_id: str

property chr: str

property interval: CytobandInterval

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

to_message() → Message

Get a protobuf representation of the class.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Allele(location: str | ChromosomeLocation | SequenceLocation, state: SequenceState | LiteralSequenceExpression | DerivedSequenceExpression | RepeatedSequenceExpression)

Bases: MessageMixin

property location: str | ChromosomeLocation | SequenceLocation

property curie: str | None

property chromosome_location: ChromosomeLocation | None

property sequence_location: SequenceLocation | None

property state: SequenceState | LiteralSequenceExpression | DerivedSequenceExpression | RepeatedSequenceExpression

property sequence_state: SequenceState | None

property literal_sequence_expression: LiteralSequenceExpression | None

property derived_sequence_expression: DerivedSequenceExpression | None

property repeated_sequence_expression: RepeatedSequenceExpression | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Haplotype(members: Iterable[Member])

Bases: MessageMixin

class Member(value: Allele | str)

Bases: MessageMixin

property value: Allele | str

property allele: Allele | None

property curie: str | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

property members: MutableSequence[Member]

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.CopyNumber(subject: Allele | Haplotype | Gene | LiteralSequenceExpression | DerivedSequenceExpression | RepeatedSequenceExpression | str, copies: Number | IndefiniteRange | DefiniteRange)

Bases: MessageMixin

property subject: Allele | Haplotype | Gene | LiteralSequenceExpression | DerivedSequenceExpression | RepeatedSequenceExpression | str

property allele: Allele | None

property haplotype: Haplotype | None

property gene: Gene | None

property literal_sequence_expression: LiteralSequenceExpression | None

property derived_sequence_expression: DerivedSequenceExpression | None

property repeated_sequence_expression: RepeatedSequenceExpression | None

property curie: str | None

property copies: Number | IndefiniteRange | DefiniteRange

property number: Number | None

property indefinite_range: IndefiniteRange | None

property definite_range: DefiniteRange | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.VariationSet(members: Iterable[Member])

Bases: MessageMixin

class Member(value: str | Allele | Haplotype | CopyNumber | Text)

Bases: MessageMixin

property value: str | Allele | Haplotype | CopyNumber | Text

property curie: str | None

property allele: Allele | None

property haplotype: Haplotype | None

property copy_number: CopyNumber | None

property text: Text | None

property variation_set

Get VariationSet if present or None if value contains a different type.

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

property members: MutableSequence[Member]

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.

class ppsc.v202.Variation(variation: Allele | Haplotype | CopyNumber | Text | VariationSet)

Bases: MessageMixin

property variation: Allele | Haplotype | CopyNumber | Text | VariationSet

property allele: Allele | None

property haplotype: Haplotype | None

property copy_number: CopyNumber | None

property text: Text | None

property variation_set: VariationSet | None

static field_names() → Iterable[str]

Get an iterable with the data class field names.

classmethod required_fields() → Sequence[str]

classmethod from_dict(values: Mapping[str, Any])

to_message() → Message

Get a protobuf representation of the class.

classmethod message_type() → Type[Message]

Get the type of the protobuf element that this class can be decoded from.

classmethod from_message(msg: Message)

Decode the message into a new instance of this class.