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onconova.oncology.models.staging

BinetStaging

Bases: Staging

Model representing the Binet staging system for oncology.

Attributes:

Name Type Description
staging OneToOneField[Staging]

A one-to-one relationship to the base Staging model
stage CodedConceptField[BinetStage]

The Binet stage value, represented as a coded concept field.

stage class-attribute instance-attribute

staging class-attribute instance-attribute

BreslowDepth

Bases: Staging

Model representing Breslow depth staging for oncology.

Attributes:

Name Type Description
staging OneToOneField[Staging]

Links to the parent Staging instance, using Breslow staging domain.
depth MeasurementField[Distance]

Breslow depth measurement of the tumor, in millimeters.
is_ulcered BooleanField

Indicates whether the primary tumor presents ulceration.
_stage_code AnnotationProperty

Annotated SNOMED code based on Breslow depth thresholds.
stage SubqueryObjectProperty[BreslowDepthStage]

Related BreslowDepthStage object, resolved by SNOMED code.

depth class-attribute instance-attribute

is_ulcered class-attribute instance-attribute

stage class-attribute instance-attribute

staging class-attribute instance-attribute

ClarkStaging

Bases: Staging

Represents the Clark staging model for oncology, extending the base Staging model.

Attributes:

Name Type Description
staging OneToOneField[Staging]

Links to the base Staging instance, using a one-to-one relationship.
stage CodedConceptField[ClarkLevel]

Stores the Clark level stage as a coded concept, referencing the ClarkLevel terminology.

stage class-attribute instance-attribute

staging class-attribute instance-attribute

FIGOStaging

Bases: Staging

methodology class-attribute instance-attribute

stage class-attribute instance-attribute

staging class-attribute instance-attribute

GleasonGrade

Bases: Staging

Represents the Gleason Grade staging model for oncology.

Attributes:

Name Type Description
staging OneToOneField[Staging]

Links to the parent Staging instance, using a one-to-one relationship.
stage CodedConceptField[GleasonGradeGroupStage]

Stores the Gleason grade stage as a coded concept, using the GleasonGradeGroupStage terminology.

stage class-attribute instance-attribute

staging class-attribute instance-attribute

INRGSSStage

Bases: Staging

Represents the INRGSS (International Neuroblastoma Risk Group Staging System) stage for neuroblastoma patients.

Attributes:

Name Type Description
staging OneToOneField[Staging]

Links to the base Staging model, with cascade deletion and a custom related name.
stage CodedConceptField[NeuroblastomaINRGSSStage]

Stores the INRGSS stage value, with terminology support for Neuroblastoma INRGSS stages.

stage class-attribute instance-attribute

staging class-attribute instance-attribute

INSSStage

Bases: Staging

Represents the International Neuroblastoma Staging System (INSS) stage for a neuroblastoma case.

Attributes:

Name Type Description
staging OneToOneField[Staging]

Link to the parent Staging instance.
stage CodedConceptField[NeuroblastomaINSSStage]

The INSS stage value, coded using the Neuroblastoma INSS terminology.

stage class-attribute instance-attribute

staging class-attribute instance-attribute

ISSStaging

Bases: Staging

ISSStaging model represents the International Staging System (ISS) staging information for oncology cases.

Attributes:

Name Type Description
staging OneToOneField[Staging]

One-to-one relationship to the base Staging model, serving as the primary key.
stage CodedConceptField[MyelomaISSStage]

Field storing the ISS stage value, using the Myeloma ISS terminology.

stage class-attribute instance-attribute

staging class-attribute instance-attribute

LymphomaStaging

Bases: Staging

Model representing the staging information for lymphoma.

Attributes:

Name Type Description
staging OneToOneField[Staging]

Link to the base Staging model, establishing a one-to-one relationship.
stage CodedConceptField[LymphomaStage]

The specific stage of lymphoma, coded using a controlled terminology.
methodology CodedConceptField[LymphomaStagingMethod]

The methodology used for determining the lymphoma stage, optional.
bulky BooleanField

Indicates the presence of bulky disease as a modifier, optional.
pathological BooleanField

Specifies whether staging was based on clinical or pathological evidence, optional.
modifiers CodedConceptField[LymphomaStageValueModifier]

Additional coded qualifiers acting as modifiers for the lymphoma stage.

bulky class-attribute instance-attribute

methodology class-attribute instance-attribute

modifiers class-attribute instance-attribute

pathological class-attribute instance-attribute

stage class-attribute instance-attribute

staging class-attribute instance-attribute

RISSStaging

Bases: Staging

Represents the Revised International Staging System (RISS) staging for oncology.

Attributes:

Name Type Description
staging OneToOneField[Staging]

Links to the base Staging model, using a one-to-one relationship.
stage CodedConceptField[MyelomaRISSStage]

Stores the RISS stage as a coded concept, using the Myeloma RISS terminology.

stage class-attribute instance-attribute

staging class-attribute instance-attribute

RaiStaging

Bases: Staging

Model representing Rai staging for oncology patients.

Attributes:

Name Type Description
staging OneToOneField[Staging]

Links to the base Staging model, ensuring a one-to-one relationship.
stage CodedConceptField[RaiStage]

Stores the Rai stage value using a coded concept field.
methodology CodedConceptField[RaiStagingMethod]

Optionally records the methodology used for Rai staging.

methodology class-attribute instance-attribute

stage class-attribute instance-attribute

staging class-attribute instance-attribute

RhabdomyosarcomaClinicalGroup

Bases: Staging

Model representing the clinical group staging for Rhabdomyosarcoma.

Attributes:

Name Type Description
staging OneToOneField[Staging]

Links to the base Staging model, ensuring a unique staging record per clinical group.
stage CodedConceptField[RhabdomyosarcomaClinicalGroup]

Stores the clinical group classification for Rhabdomyosarcoma, using controlled terminology.

stage class-attribute instance-attribute

staging class-attribute instance-attribute

Staging

Bases: BaseModel

Represents a staging record for a patient's cancer case, encapsulating the domain-specific staging information.

Attributes:

Name Type Description
case ForeignKey[PatientCase]

Reference to the PatientCase being staged.
date DateField

Date when the staging was performed and recorded.
staged_entities ManyToManyField[NeoplasticEntity]

References to neoplastic entities involved in the staging.
description str

Human-readable description of the staging, combining domain and stage value.
stage_value str | None

Extracted stage value from the domain-specific staging display string.
staging_domain str | None

The domain key corresponding to the staging information present.

STAGING_DOMAINS class-attribute instance-attribute

case class-attribute instance-attribute

date class-attribute instance-attribute

description property

stage_value property

staged_entities class-attribute instance-attribute

staging_domain property

get_domain_staging()

Source code in onconova/oncology/models/staging.py 
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def get_domain_staging(self) -> type["Staging"] | None:
    if self.staging_domain:
        return getattr(self, self.staging_domain)
    else:
        return None

StagingDomain

Bases: TextChoices

Enumeration of cancer staging domains used in oncology.

Each member represents a specific staging system or classification used to describe the extent or severity of cancer. The available staging domains include:

  • TNM: Tumor, Node, Metastasis staging system.
  • FIGO: International Federation of Gynecology and Obstetrics staging.
  • BINET: Binet staging for chronic lymphocytic leukemia.
  • RAI: Rai staging for chronic lymphocytic leukemia.
  • BRESLOW: Breslow thickness for melanoma.
  • CLARK: Clark level for melanoma.
  • ISS: International Staging System for multiple myeloma.
  • RISS: Revised International Staging System for multiple myeloma.
  • INSS: International Neuroblastoma Staging System.
  • INRGSS: International Neuroblastoma Risk Group Staging System.
  • GLEASON: Gleason grading for prostate cancer.
  • RHABDO: Staging for rhabdomyosarcoma.
  • WILMS: Staging for Wilms tumor.
  • LYMPHOMA: Staging for lymphoma.

This enumeration is used to standardize staging domain references throughout the application.

BINET class-attribute instance-attribute

BRESLOW class-attribute instance-attribute

CLARK class-attribute instance-attribute

FIGO class-attribute instance-attribute

GLEASON class-attribute instance-attribute

INRGSS class-attribute instance-attribute

INSS class-attribute instance-attribute

ISS class-attribute instance-attribute

LYMPHOMA class-attribute instance-attribute

RAI class-attribute instance-attribute

RHABDO class-attribute instance-attribute

RISS class-attribute instance-attribute

TNM class-attribute instance-attribute

WILMS class-attribute instance-attribute

TNMStaging

Bases: Staging

Model representing TNM cancer staging information.

Attributes:

Name Type Description
staging OneToOneField[Staging]

Link to the base Staging instance.
stage CodedConceptField[TNMStage]

TNM stage classification.
methodology CodedConceptField[TNMStagingMethod]

Methodology used for TNM staging.
pathological BooleanField

Indicates if staging is pathological (True) or clinical (False).
primaryTumor CodedConceptField[TNMPrimaryTumorCategory]

T stage (extent of the primary tumor).
regionalNodes CodedConceptField[TNMRegionalNodesCategory]

N stage (spread to regional lymph nodes).
distantMetastases CodedConceptField[TNMDistantMetastasesCategory]

M stage (presence of distant metastasis).
grade CodedConceptField[TNMGradeCategory]

G stage (grade of cancer cells).
residualTumor CodedConceptField[TNMResidualTumorCategory]

R stage (extent of residual tumor cells post-operation).
lymphaticInvasion CodedConceptField[TNMLymphaticInvasionCategory]

L stage (lymphatic vessel invasion).
venousInvasion CodedConceptField[TNMVenousInvasionCategory]

V stage (venous vessel invasion).
perineuralInvasion CodedConceptField[TNMPerineuralInvasionCategory]

Pn stage (adjunct nerve invasion).
serumTumorMarkerLevel CodedConceptField[TNMSerumTumorMarkerLevelCategory]

S stage (serum tumor marker level).

distantMetastases class-attribute instance-attribute

grade class-attribute instance-attribute

lymphaticInvasion class-attribute instance-attribute

methodology class-attribute instance-attribute

pathological class-attribute instance-attribute

perineuralInvasion class-attribute instance-attribute

primaryTumor class-attribute instance-attribute

regionalNodes class-attribute instance-attribute

residualTumor class-attribute instance-attribute

serumTumorMarkerLevel class-attribute instance-attribute

stage class-attribute instance-attribute

staging class-attribute instance-attribute

venousInvasion class-attribute instance-attribute

WilmsStage

Bases: Staging

Model representing the staging information for Wilms tumor.

Attributes:

Name Type Description
staging OneToOneField[Staging]

Links to the base Staging model, with cascade deletion and a custom related name.
stage CodedConceptField[WilmsTumorStage]

Stores the Wilms tumor stage, using a controlled terminology.

stage class-attribute instance-attribute

staging class-attribute instance-attribute

runner