Oncopacket: Model Module

The model module of Oncopacket contains data models that represent cancer patient data. These models can be constructed with data from various upstream sources and then exported in GA4GH Phenopacket format.

Core Classes

The model module includes several key classes:

OpIndividual

The OpIndividual class represents a cancer patient, with demographic information, disease diagnoses, biosamples, and genetic variants.

API Documentation for OpIndividual

OpDisease

The OpDisease class represents cancer diagnoses, including cancer type, stage, grade, and other diagnostic information.

OpMutation

The OpMutation class represents genetic mutations/variants found in a patient's tumor samples.

Usage Example

from oncopacket.model import OpIndividual
import phenopackets as PPkt

# Create vital status object
vital_status = PPkt.VitalStatus()
vital_status.status = PPkt.VitalStatus.ALIVE

# Create an individual
individual = OpIndividual(
    id="TCGA-12345",
    sex="FEMALE",
    iso8601duration="P65Y",  # 65 years old
    vital_status=vital_status
)

# Convert to GA4GH Phenopacket Individual
ga4gh_individual = individual.to_ga4gh()

Note that the to_ga4gh() method only converts the individual information to a GA4GH format. For creating complete phenopackets with disease and mutation information, you should use the factory classes provided in the CDA module.

Integration with CDA

The model classes are populated by the factory classes in the CDA module, which extract data from the Cancer Data Aggregator API and convert it to the appropriate model objects.