CytoTargetDB/object_classes.py at main · MorrissyLab/CytoTargetDB · GitHub

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#Object definitions for clinical trial data

from typing import TypedDict, List, Literal, Optional

class Target(TypedDict):
    # Annotated fields

    #gene info
    gene: str #ai annotated gene name, not necessarily official symbol
    gene_symbol: str
    HGNC_id: str

    #binding and cytotoxicity
    antigen_ligand: str
    binding_type: str
    cytotoxicity: str
    cytotoxicity_type: str
    cytotoxicity_mechanism: str

    #modifiers
    enzyme_product: bool
    epitope: bool
    variant: bool
    isoform: bool
    HLA_specific: bool
    gated: bool
    other_modifier: Optional[str]

class Drug(TypedDict):
    # Source fields from associated intervention object
    drug_name: str
    intervention_type: str
    drug_description: str

    # Annotated fields

    type: Literal[
        "RELEVANT_DRUG",
        "NOT_RELEVANT_DRUG"
        ]

    # Drug mapping
    NCI_thesaurus_concept_id: Optional[str]
    NCI_thesaurus_preferred_term: Optional[str]
    NCI_thesaurus_definition: Optional[str]
    drug_mesh_term: Optional[str]

    # Categorizations
    drug_category: Optional[str]
    drug_class: Optional[str]

    # Delivery route
    drug_delivery_route: Optional[str]

    # Mechanism of action
    drug_mechanism_of_action: Optional[str]

    # Targets
    targets: Optional[List[Target]]  # LIST OF OBJECTS


class Disease(TypedDict):
    # Annotated fields

    # Disease categorization
    type: Literal[
        "CANCER",
        "NON-CANCER"
        ]

    # Disease name and tissue
    disease_name: str
    tissue_type: str

    # Disease mapping
    disease_mesh_term: Optional[str]
    Oncotree_name: Optional[str]
    Oncotree_mainType: Optional[str]

class Intervention(TypedDict):
    #Source fields
    type: str
    name: str
    description: str
    arm_group_labels: List[str] # LIST
    other_names: List[str] # LIST

class ArmGroup(TypedDict):
    #Source fields
    label: str
    type: str
    description: str
    intervention_names: List[str] # LIST
    drugs: Optional[List[Drug]]  # LIST OF OBJECTS

class ClinicalTrial(TypedDict):
    type: Literal[
        "IMMUNOTHERAPY",
        "NOT_IMMUNOTHERAPY"
        ]

    # Core identification
    nct_id: str
    brief_title: str
    official_title: str

    # Study description
    brief_summary: str
    detailed_description: str
    conditions: List[str] # LIST
    condition_mesh_terms: List[str] # LIST
    keywords: List[str] # LIST

    # Study design
    study_type: str

    # Study arms and interventions
    arm_groups: List[ArmGroup] # LIST OF OBJECTS
    interventions: List[Intervention] # LIST OF OBJECTS
    intervention_mesh_terms: List[str]  # LIST

    # Eligibility
    eligibility_criteria: str

    #annotation tracking
    trial_source: Optional[str]
    annotation_status: Optional[str]

    #annotation
    ai_summary: Optional[str]
    eligibility_summary: Optional[str]
    annotation_time_seconds: Optional[float]
    drugs: List[Drug] # LIST OF OBJECTS
    diseases: List[Disease] # LIST OF OBJECTS