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onconova.interoperability.fhir.models.GenomicVariant

NoneType module-attribute

AnnotationCode

Bases: Extension

Codifies the content of an Annotation

extension class-attribute instance-attribute

url class-attribute instance-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

FHIR_url_fixed_value_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('url',), mode="after", check_fields=None)
@classmethod
def FHIR_url_fixed_value_constraint(cls, value):    
    return validate_FHIR_element_fixed_value(cls, value, 
        constant='http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code',
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('extension',), mode="after", check_fields=None)
@classmethod
def extension_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="extension",
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=False,
    )

BodyStructureReference

Bases: Extension

Record details about the anatomical location of a specimen or body part. This resource may be used when a coded concept does not provide the necessary detail needed for the use case.

extension class-attribute instance-attribute

url class-attribute instance-attribute

value property

valueReference class-attribute instance-attribute

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

FHIR_url_fixed_value_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('url',), mode="after", check_fields=None)
@classmethod
def FHIR_url_fixed_value_constraint(cls, value):    
    return validate_FHIR_element_fixed_value(cls, value, 
        constant='http://hl7.org/fhir/StructureDefinition/bodySite',
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('extension',), mode="after", check_fields=None)
@classmethod
def extension_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="extension",
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Reference'],
        field_name_base="value",
        required=True,
    )

CodedAnnotation

Bases: Annotation

A text note which also contains information about who made the statement and when.

extension class-attribute instance-attribute

FHIR_ele_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ele_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='hasValue() or (children().count() > id.count())',
        human='All FHIR elements must have a @value or children',
        key='ele-1',
        severity='error',
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('extension',), mode="after", check_fields=None)
@classmethod
def extension_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="extension",
    )

CodedAnnotationCode

Bases: AnnotationCode, FHIRSliceModel

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

max_cardinality class-attribute

min_cardinality class-attribute

FHIR_ele_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ele_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='hasValue() or (children().count() > id.count())',
        human='All FHIR elements must have a @value or children',
        key='ele-1',
        severity='error',
    )

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

GenomicFinding

Bases: GenomicsBase

Measurements and simple assertions made about a patient, device or other subject.

component class-attribute instance-attribute

FHIR_obs_6_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_obs_6_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='dataAbsentReason.empty() or value.empty()',
        human='dataAbsentReason SHALL only be present if Observation.value[x] is not present',
        key='obs-6',
        severity='error',
    )

FHIR_obs_7_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_obs_7_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()',
        human='If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present',
        key='obs-7',
        severity='error',
    )

component_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('component',), mode="after", check_fields=None)
@classmethod
def component_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="component",
    )

GenomicFindingCytogeneticLocation

Bases: ObservationComponent, FHIRSliceModel

The relevant chromosomal region. The combination of numbers and letters provide a genetic 'address'.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='48001-2', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

GenomicFindingGeneStudied

Bases: ObservationComponent, FHIRSliceModel

The gene(s) on which the variant is located.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='48018-6', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

GenomicFindingReferenceSequenceAssembly

Bases: ObservationComponent, FHIRSliceModel

The reference genome/assembly used in this analysis.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='62374-4', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

GenomicVariant

Bases: Variant

Measurements and simple assertions made about a patient, device or other subject.

category class-attribute instance-attribute

component class-attribute instance-attribute

dataAbsentReason class-attribute instance-attribute

effective property

effectiveDateTime class-attribute instance-attribute

effectiveInstant class-attribute instance-attribute

effectivePeriod class-attribute instance-attribute

effectiveTiming class-attribute instance-attribute

hasMember class-attribute instance-attribute

referenceRange class-attribute instance-attribute

specimen class-attribute instance-attribute

status class-attribute instance-attribute

subject class-attribute instance-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='69548-6', system='http://loinc.org')]),
    )

FHIR_obs_3_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_obs_3_constraint_validator(self):
    return validate_element_constraint( 
        self,
        elements="referenceRange",
        expression='low.exists() or high.exists() or text.exists()',
        human='Must have at least a low or a high or text',
        key='obs-3',
        severity='error',
    )

FHIR_obs_6_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_obs_6_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='dataAbsentReason.empty() or value.empty()',
        human='dataAbsentReason SHALL only be present if Observation.value[x] is not present',
        key='obs-6',
        severity='error',
    )

FHIR_obs_7_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_obs_7_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()',
        human='If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present',
        key='obs-7',
        severity='error',
    )

category_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('category',), mode="after", check_fields=None)
@classmethod
def category_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="category",
    )

component_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('component',), mode="after", check_fields=None)
@classmethod
def component_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="component",
    )

effective_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def effective_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['DateTime', 'Period', 'Timing', 'Instant'],
        field_name_base="effective",
        required=False,
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantAllelicState

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantAminoAcidChangeType

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantAssessmentDate

Bases: Extension

Date at which the genomic variant was assessed and/or reported.

extension class-attribute instance-attribute

url class-attribute instance-attribute

value property

valueDateTime class-attribute instance-attribute

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

FHIR_url_fixed_value_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('url',), mode="after", check_fields=None)
@classmethod
def FHIR_url_fixed_value_constraint(cls, value):    
    return validate_FHIR_element_fixed_value(cls, value, 
        constant='http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date',
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('extension',), mode="after", check_fields=None)
@classmethod
def extension_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="extension",
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['DateTime'],
        field_name_base="value",
        required=False,
    )

GenomicVariantCodingChangeType

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantCopyNumber

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantCytogeneticLocation

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantCytogenomicNomenclature

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantGeneStudied

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantGenomicHgvs

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantGenomicSourceClass

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantLabCategory

Bases: CodeableConcept, FHIRSliceModel

A code that classifies the general type of observation being made.

coding class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

FHIR_Category_pattern_constraint()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_Category_pattern_constraint(self):
    return validate_FHIR_model_pattern( 
        self,
        pattern=CodeableConcept(coding=[Coding(code='laboratory', system='http://terminology.hl7.org/CodeSystem/observation-category')]),
    )

FHIR_coding_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('coding',), mode="after", check_fields=None)
@classmethod
def FHIR_coding_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=Coding(code='laboratory', system='http://terminology.hl7.org/CodeSystem/observation-category'),
    )

GenomicVariantMolecularConsequence

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantProteinHgvs

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantSampleAllelicFrequency

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicVariantVariationCode

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

GenomicsBase

Bases: Observation

Measurements and simple assertions made about a patient, device or other subject.

category class-attribute instance-attribute

component class-attribute instance-attribute

extension class-attribute instance-attribute

note class-attribute instance-attribute

FHIR_obs_6_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_obs_6_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='dataAbsentReason.empty() or value.empty()',
        human='dataAbsentReason SHALL only be present if Observation.value[x] is not present',
        key='obs-6',
        severity='error',
    )

FHIR_obs_7_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_obs_7_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()',
        human='If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present',
        key='obs-7',
        severity='error',
    )

category_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('category',), mode="after", check_fields=None)
@classmethod
def category_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="category",
    )

component_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('component',), mode="after", check_fields=None)
@classmethod
def component_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="component",
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('extension',), mode="after", check_fields=None)
@classmethod
def extension_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="extension",
    )

GenomicsBaseBodyStructure

Bases: BodyStructureReference, FHIRSliceModel

May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

max_cardinality class-attribute

min_cardinality class-attribute

FHIR_ele_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ele_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='hasValue() or (children().count() > id.count())',
        human='All FHIR elements must have a @value or children',
        key='ele-1',
        severity='error',
    )

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

GenomicsBaseConclusionString

Bases: ObservationComponent, FHIRSliceModel

Concise and clinically contextualized summary conclusion (interpretation/impression) of the observation

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueString class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='conclusion-string', system='http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['String'],
        field_name_base="value",
        required=False,
    )

GenomicsBaseLabCategory

Bases: CodeableConcept, FHIRSliceModel

A code that classifies the general type of observation being made.

coding class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

FHIR_coding_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('coding',), mode="after", check_fields=None)
@classmethod
def FHIR_coding_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=Coding(code='laboratory', system='http://terminology.hl7.org/CodeSystem/observation-category'),
    )

GenomicsBaseSecondaryFinding

Bases: SecondaryFinding, FHIRSliceModel

May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

max_cardinality class-attribute

min_cardinality class-attribute

FHIR_ele_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ele_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='hasValue() or (children().count() > id.count())',
        human='All FHIR elements must have a @value or children',
        key='ele-1',
        severity='error',
    )

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

OnconovaGenomicVariant

Bases: GenomicVariant

Measurements and simple assertions made about a patient, device or other subject.

bodySite class-attribute instance-attribute

component class-attribute instance-attribute

device class-attribute instance-attribute

effective property

encounter class-attribute instance-attribute

extension class-attribute instance-attribute

focus class-attribute instance-attribute

interpretation class-attribute instance-attribute

issued class-attribute instance-attribute

performer class-attribute instance-attribute

specimen class-attribute instance-attribute

status class-attribute instance-attribute

FHIR_o_var_req_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_o_var_req_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='subject.exists()',
        human='The subject element is required and must be provided.',
        key='o-var-req-1',
        severity='error',
    )

FHIR_o_var_req_2_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_o_var_req_2_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='effectiveDateTime.exists() and effectiveDateTime.hasValue()',
        human='The effectiveDateTime element is required and must be provided.',
        key='o-var-req-2',
        severity='error',
    )

FHIR_o_var_req_3_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_o_var_req_3_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression="component.where(code.coding.code = '48018-6').exists()",
        human='The genes extension is required and must be provided.',
        key='o-var-req-3',
        severity='error',
    )

FHIR_o_var_req_4_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_o_var_req_4_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression="component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()",
        human='At least one HGVS representation (coding, protein, or genomic) must be provided.',
        key='o-var-req-4',
        severity='error',
    )

component_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('component',), mode="after", check_fields=None)
@classmethod
def component_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="component",
    )

effective_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def effective_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['DateTime'],
        field_name_base="effective",
        required=True,
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('extension',), mode="after", check_fields=None)
@classmethod
def extension_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="extension",
    )

OnconovaGenomicVariantAllelicReadDepth

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantAllelicState

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantAltAllele

Bases: ObservationComponent, FHIRSliceModel

Not used in this profile

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantAminoAcidChangeType

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

OnconovaGenomicVariantChromosomeIdentifier

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantClinicalRelevance

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='LL4034-6', display='ACMG_Clinical significance of genetic variation', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=False,
    )

OnconovaGenomicVariantCodingChangeType

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

OnconovaGenomicVariantCodingHgvs

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

OnconovaGenomicVariantConclusionString

Bases: ObservationComponent, FHIRSliceModel

Not used in this profile

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantCoordinateSystem

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantCopyNumber

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantCytogeneticLocation

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantExactStartEnd

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantGenePanelSequencing

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueString class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='C165600', display='Tumor Panel Sequencing', system='http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['String'],
        field_name_base="value",
        required=False,
    )

OnconovaGenomicVariantGeneRegion

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueString class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='C13445', display='Gene Feature', system='http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['String'],
        field_name_base="value",
        required=False,
    )

OnconovaGenomicVariantGenomicHgvs

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

OnconovaGenomicVariantGenomicRefSeq

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantGenomicSourceClass

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantGenomicVariantAssessmentDate

Bases: GenomicVariantAssessmentDate, FHIRSliceModel

May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

max_cardinality class-attribute

min_cardinality class-attribute

FHIR_ele_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ele_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='hasValue() or (children().count() > id.count())',
        human='All FHIR elements must have a @value or children',
        key='ele-1',
        severity='error',
    )

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

OnconovaGenomicVariantHgvsVersion

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueString class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='81303-0', display='HGVS version [ID]', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['String'],
        field_name_base="value",
        required=False,
    )

OnconovaGenomicVariantInnerStartEnd

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantMolecularConsequence

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantNucleotidesCount

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueInteger class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='C709', display='Nucleotides', system='http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Integer'],
        field_name_base="value",
        required=False,
    )

OnconovaGenomicVariantOuterStartEnd

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantProteinHgvs

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueBoolean class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

valueDateTime class-attribute instance-attribute

valueInteger class-attribute instance-attribute

valuePeriod class-attribute instance-attribute

valueQuantity class-attribute instance-attribute

valueRange class-attribute instance-attribute

valueRatio class-attribute instance-attribute

valueSampledData class-attribute instance-attribute

valueString class-attribute instance-attribute

valueTime class-attribute instance-attribute

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity', 'CodeableConcept', 'String', 'Boolean', 'Integer', 'Range', 'Ratio', 'SampledData', 'Time', 'DateTime', 'Period'],
        field_name_base="value",
        required=False,
    )

OnconovaGenomicVariantRefAllele

Bases: ObservationComponent, FHIRSliceModel

Not used in this profile

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantReferenceSequenceAssembly

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantRnaHgvs

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='rna-hgvs', display='Transcript RNA change (rHGVS)', system='http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=False,
    )

OnconovaGenomicVariantSampleAllelicFrequency

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantTranscriptRefSeq

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantVariantConfidenceStatus

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantVariantInheritance

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

OnconovaGenomicVariantVariationCode

Bases: ObservationComponent, FHIRSliceModel

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

max_cardinality class-attribute

min_cardinality class-attribute

SecondaryFinding

Bases: Extension

Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.

For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings.

extension class-attribute instance-attribute

url class-attribute instance-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_ext_1_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_ext_1_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='extension.exists() != value.exists()',
        human='Must have either extensions or value[x], not both',
        key='ext-1',
        severity='error',
    )

FHIR_url_fixed_value_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('url',), mode="after", check_fields=None)
@classmethod
def FHIR_url_fixed_value_constraint(cls, value):    
    return validate_FHIR_element_fixed_value(cls, value, 
        constant='http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding',
    )

extension_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('extension',), mode="after", check_fields=None)
@classmethod
def extension_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="extension",
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
59
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

Variant

Bases: GenomicFinding

Measurements and simple assertions made about a patient, device or other subject.

code class-attribute instance-attribute

component class-attribute instance-attribute

method class-attribute instance-attribute

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='69548-6', system='http://loinc.org')]),
    )

FHIR_obs_6_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_obs_6_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='dataAbsentReason.empty() or value.empty()',
        human='dataAbsentReason SHALL only be present if Observation.value[x] is not present',
        key='obs-6',
        severity='error',
    )

FHIR_obs_7_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_obs_7_constraint_validator(self):
    return validate_model_constraint( 
        self,
        expression='value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()',
        human='If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present',
        key='obs-7',
        severity='error',
    )

component_slicing_cardinality_validator(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('component',), mode="after", check_fields=None)
@classmethod
def component_slicing_cardinality_validator(cls, value):    
    return validate_slicing_cardinalities(cls, value, 
        field_name="component",
    )

VariantAllelicReadDepth

Bases: ObservationComponent, FHIRSliceModel

Specifies the number of reads that identified the allele in question whether it consists of one or a small sequence of contiguous nucleotides. Different methods and purposes require different numbers of reads to be acceptable. Often >400, sometimes as few as 2-4.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueQuantity class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
1215
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='82121-5', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity'],
        field_name_base="value",
        required=False,
    )

VariantAllelicState

Bases: ObservationComponent, FHIRSliceModel

The observed level of occurrence of the variant in the set of chromosomes.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
1255
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='53034-5', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantAltAllele

Bases: ObservationComponent, FHIRSliceModel

The genomic alternate allele is the contiguous segment of DNA in the test sample that differs from the reference allele at the same location and thus defines a variant.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueString class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
1036
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='69551-0', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['String'],
        field_name_base="value",
        required=False,
    )

VariantAminoAcidChangeType

Bases: ObservationComponent, FHIRSliceModel

Codified type for associated Amino Acid Marker, for convenience.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='48006-1', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantChromosomeIdentifier

Bases: ObservationComponent, FHIRSliceModel

An indicator, enumerated in humans by numbers 1-22, X, and Y, representing the chromosome on which the variant is located.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='48000-4', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantCodingChangeType

Bases: ObservationComponent, FHIRSliceModel

Type of DNA change observed. Convenience property for variants with exact breakpoints, required otherwise.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='48019-4', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantCodingHgvs

Bases: ObservationComponent, FHIRSliceModel

Description of the coding (cDNA) sequence change using a valid HGVS-formatted string.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='48004-6', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantCoordinateSystem

Bases: ObservationComponent, FHIRSliceModel

These are different ways of identifying nucleotides or amino acids within a sequence. In the 1-based system, the first unit of the polymer (e.g. the first nucleotide) is counted as number 1. In the 0-based system, the number 0 designates the location before the first nucleotide. Different databases and file types may use different systems.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='92822-6', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantCopyNumber

Bases: ObservationComponent, FHIRSliceModel

The copy number of the large variant. In HGVS, this is the numeric value following the “X”. It is a unit-less value. Note that a copy number of 1 can imply a deletion.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueQuantity class-attribute instance-attribute

FHIR_cnt_3_constraint_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def FHIR_cnt_3_constraint_validator(self):
    return validate_element_constraint( 
        self,
        elements="valueQuantity",
        expression="(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())",
        human="There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number.",
        key='cnt-3',
        severity='error',
    )

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='82155-3', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity'],
        field_name_base="value",
        required=False,
    )

VariantCytogenomicNomenclature

Bases: ObservationComponent, FHIRSliceModel

Fully describes a variant with a single code. Typically a large variant such as a mosaic, abnormal chromosome numbers, etc.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='81291-7', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantExactStartEnd

Bases: ObservationComponent, FHIRSliceModel

The exact integer-based genomic coordinates of the start and end of the variant region.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueRange class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='81254-5', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Range'],
        field_name_base="value",
        required=False,
    )

VariantGenomicHgvs

Bases: ObservationComponent, FHIRSliceModel

Description of the genomic (gDNA) sequence change using a valid HGVS-formatted string.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='81290-9', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantGenomicRefSeq

Bases: ObservationComponent, FHIRSliceModel

ID of the genomic reference sequence, which includes transcribed and non transcribed stretches

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='48013-7', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantGenomicSourceClass

Bases: ObservationComponent, FHIRSliceModel

The genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='48002-0', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantInnerStartEnd

Bases: ObservationComponent, FHIRSliceModel

The genomic coordinates of the narrowest genomic range in which the variant might reside. Used when the exact boundaries of the variant are not clear.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueRange class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='81302-2', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Range'],
        field_name_base="value",
        required=False,
    )

VariantMolecularConsequence

Bases: ObservationComponent, FHIRSliceModel

The calculated or observed effect of a variant on its downstream transcript and, if applicable, ensuing protein sequence.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='molecular-consequence', system='http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantOuterStartEnd

Bases: ObservationComponent, FHIRSliceModel

The genomic coordinates of the widest genomic range in which the variant might reside. Used when the exact boundaries of the variant are not clear.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueRange class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='81301-4', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Range'],
        field_name_base="value",
        required=False,
    )

VariantProteinHgvs

Bases: ObservationComponent, FHIRSliceModel

Description of the protein (amino acid) sequence change using a valid HGVS-formatted string. The description of the variant is surrounded in parentheses if it is calculated rather than directly observed.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='48005-3', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantRefAllele

Bases: ObservationComponent, FHIRSliceModel

Reference values ('normal') examined within the Reference Sequence.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueString class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='69547-8', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['String'],
        field_name_base="value",
        required=False,
    )

VariantSampleAllelicFrequency

Bases: ObservationComponent, FHIRSliceModel

The relative frequency of the allele at a given locus in the sample.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueQuantity class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='81258-6', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['Quantity'],
        field_name_base="value",
        required=False,
    )

VariantTranscriptRefSeq

Bases: ObservationComponent, FHIRSliceModel

NCBI's RefSeq ('NM_...'), Ensembl ('ENST...'), and LRG ('LRG...' plus 't1' to indicate transcript)

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='51958-7', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantValueQuantity

Bases: Quantity

The information determined as a result of making the observation, if the information has a simple value.

system class-attribute instance-attribute

FHIR_system_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('system',), mode="after", check_fields=None)
@classmethod
def FHIR_system_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern='http://unitsofmeasure.org',
    )

VariantVariantConfidenceStatus

Bases: ObservationComponent, FHIRSliceModel

A code that represents the confidence of a true positive variant call.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='variant-confidence-status', system='http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantVariantInheritance

Bases: ObservationComponent, FHIRSliceModel

By which parent the variant was inherited in the patient, if known.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='variant-inheritance', system='http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )

VariantVariationCode

Bases: ObservationComponent, FHIRSliceModel

Accession number in a variant database such as ClinVar, given for cross-reference.

code class-attribute instance-attribute

max_cardinality class-attribute

min_cardinality class-attribute

value property

valueCodeableConcept class-attribute instance-attribute

FHIR_code_pattern_constraint(value) classmethod

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@field_validator(*('code',), mode="after", check_fields=None)
@classmethod
def FHIR_code_pattern_constraint(cls, value):    
    return validate_FHIR_element_pattern(cls, value, 
        pattern=CodeableConcept(coding=[Coding(code='81252-9', system='http://loinc.org')]),
    )

value_type_choice_validator()

Source code in onconova/interoperability/fhir/models/GenomicVariant.py 
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@model_validator(mode="after")
def value_type_choice_validator(self):
    return validate_type_choice_element( 
        self,
        field_types=['CodeableConcept'],
        field_name_base="value",
        required=True,
    )
runner